Merge lp:~kumbarov/ubuntu/trusty/phylip/phylip-fix-1440240 into lp:ubuntu/trusty/phylip

[Kumbarov]

The CFLAGS variable in the make file is left empty which results in compiling the source code without optimization flags. I uncommented the line which sets the optimization flags. By compiling the source with optimisation flags, the program executes twice as fast.

[Sebastien Bacher (seb128)]

thanks, the change is in wily now, it could be backported to trusty but somebody needs to follow the SRU instructions on https://wiki.ubuntu.com/StableReleaseUpdates

the current changes need work, the diff include a new version which is not required to fix the issue, ideally somebody would backport the debian change with a changelog explaining what is done

review: Needs Fixing

Unmerged revisions

9. By Kumbarov on 2015-04-04

Use optimization flags by default when compiling

8. By Andreas Tille on 2014-09-17

* New upstream version now with free license
* cme fix dpkg-control
* removed redundant README.source
* d/copyright:
   - DEP5 now with BSD-2-Clause license
   - exclude some binaries without source which are not needed
* Add bash_completion

=== modified file '.pc/01_src_phylip_h/src/phylip.h'
--- .pc/01_src_phylip_h/src/phylip.h	2013-08-07 22:17:03 +0000
+++ .pc/01_src_phylip_h/src/phylip.h	2015-04-04 21:58:41 +0000
@@ -1,13 +1,37 @@
 #ifndef _PHYLIP_H_
 #define _PHYLIP_H_
 
-/* version 3.6. (c) Copyright 1993-2004 by the University of Washington.
+/* version 3.696.
    Written by Joseph Felsenstein, Akiko Fuseki, Sean Lamont, Andrew Keeffe,
    Mike Palczewski, Doug Buxton and Dan Fineman.
-   Permission is granted to copy and use this program provided no fee is
-   charged for it and provided that this copyright notice is not removed. */
-
-#define VERSION "3.695"
+
+   Copyright (c) 1980-2014, Joseph Felsenstein
+   All rights reserved.
+
+   Redistribution and use in source and binary forms, with or without
+   modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice,
+      this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice,
+      this list of conditions and the following disclaimer in the documentation
+      and/or other materials provided with the distribution.
+
+   THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
+   AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
+   IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
+   ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE 
+   LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
+   CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
+   SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
+   INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
+   CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
+   ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
+   POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#define VERSION "3.696"
 
 /* Debugging options */
 /* Define this to disable assertions */
@@ -199,17 +223,6 @@
 #include <math.h>
 #include <ctype.h>
 
-/*
-#ifdef MAC
-#ifdef DRAW
-#include "interface.h"
-#else
-#include "macface.h"
-#endif
-#define getch gettch
-#endif
-*/
-
 /* directory delimiters */
 #ifdef MAC
 #define DELIMITER ':'

=== modified file '.pc/applied-patches'
--- .pc/applied-patches	2013-08-07 22:17:03 +0000
+++ .pc/applied-patches	2015-04-04 21:58:41 +0000
@@ -1,3 +1,5 @@
 install_fonts_data.patch
 hardening.patch
 01_src_phylip_h
+do_not_install_jar_files.patch
+soname.patch

=== added directory '.pc/do_not_install_jar_files.patch'
=== added directory '.pc/do_not_install_jar_files.patch/src'
=== added file '.pc/do_not_install_jar_files.patch/src/Makefile.unx'
--- .pc/do_not_install_jar_files.patch/src/Makefile.unx	1970-01-01 00:00:00 +0000
+++ .pc/do_not_install_jar_files.patch/src/Makefile.unx	2015-04-04 21:58:41 +0000
@@ -0,0 +1,615 @@
+# Makefile
+#
+# Unix Makefile for PHYLIP 3.696
+
+PACKAGE=phylip
+VERSION=3.696
+
+# We use GNU's version of the make utility. It may be called "gmake" on
+# your system.
+#
+# If you're using a RedHat Linux system with default locations for 
+# gcc libraries, you probably don't need to change anything. You might
+# might change the first noncomment statement below to redefine $(EXEDIR)
+# if you'd like your executables installed in a different location than
+# our default.
+#
+# Users with systems that differ substantially from ours may need to set
+# the following variables: $(CC) $(CFLAGS) $(DFLAGS) $(LIBS) $(DLIBS)
+#
+# When uncompressed and extracted, the tar archive phylip-3.6x.tar.gz 
+# produces the following directory structure:
+#
+#   phylip-3.6x/src -- the source code, including this Makefile
+#   phylip-3.6x/exe -- executables, changed by changing $(EXEDIR) value
+#   phylip-3.6x/doc -- html documentation
+#
+#  To use the PHYLIP v3.6 Makefile, type from the phylip-3.6x/src directory:
+#
+#      make install         to compile the whole package and install
+#                           the executables in $(EXEDIR), and then
+#                           remove the object files to save space
+#
+#      make all             to compile the whole package but not install it
+#                           or remove the object files. 
+#
+#      make put             to move the executables into $(EXEDIR)
+#
+#      make clean           to remove all object files and executables from the
+#                           current directory
+#
+#      make dnaml           to compile and link one program, (in this example,
+#                           DnaML) and leave the executable and object files
+#                           in the current directory (where the source code is).
+#                           You will have to move the executable into the
+#                           executables directory (e.g. "mv dnaml ../exe")
+#                           Note that the program name should be lower case.
+# 
+# ----------------------------------------------------------------------------
+#  (Starting here is the section where you may want to change things)
+# ----------------------------------------------------------------------------
+#
+# the following specifies the directory where the executables will be placed
+EXEDIR  = ../exe
+DATADIR = ../exe
+#
+# ----------------------------------------------------------------------------
+#
+# The following statements set these variables:
+#
+#    CC     -- the name (and, optionally, location) of your C compiler
+#    CFLAGS -- compiler directives needed to compile most programs
+#    DFLAGS -- compiler directives needed to compile draw programs
+#    LIBS   -- non-default system libraries needed to compile most programs
+#    DLIBS  -- non-default system libraries needed to compile draw programs
+#
+# We've provided a set of possible values for each variable.
+#
+# The value used is the one without a "#" at the beginning of the line.
+#
+# To try an alternate value, make sure the one you want has no "#"
+# as its first character and that all other possibilities have "#" for
+# their first character.
+#
+# Advanced users may need to further edit one of the alternatives in
+# order to correctly compile on their system.
+#
+# ----------------------------------------------------------------------------
+#
+# The next two assignments are the invocations of the compiler
+#
+# This one specifies the "cc" C compiler
+#CC        = cc
+#
+#  To use GCC instead:
+CC        = gcc
+#
+# ----------------------------------------------------------------------------
+#
+# This is the CFLAGS statement. It specifies compiler behavior.
+#
+# Here are some possible CFLAGS statements:
+#
+#
+#A minimal one
+CFLAGS =
+#
+# A basic one for debugging
+#CFLAGS  = -g 
+#
+# An optimized one for gcc
+#CFLAGS  = -O3 -DUNX -fomit-frame-pointer
+#
+# For some serious debugging using Gnu gcc
+#
+#CFLAGS=-g -DUNX -Wall -Wmain -Wmissing-prototypes -Wreturn-type -Wstrict-prototypes  -Wunused -Werror -Wredundant-decls -Waggregate-return -Wcast-align -Wcomment
+#
+# For doing code coverage with gcov
+#
+#CFLAGS	=	-ggdb -DUNX -fprofile-arcs -ftest-coverage
+#CFLAGS	=	-pg -DUNX
+#
+# For Digital Alpha systems with Compaq Tru64 Unix
+# (however, be aware that this may cause floating-point problems in programs
+#  like Dnaml owing to not using IEEE floating point standards).
+#CFLAGS = -fast -DUNX
+#
+# ----------------------------------------------------------------------------
+#
+# This is the DFLAGS statement. It specifies compiler behavior for the
+# programs drawgram and drawtree. It adds additional information to
+# the $(CFLAGS) value if needed.
+#
+DFLAGS = $(CFLAGS)
+#
+# ----------------------------------------------------------------------------
+#
+# Most of the programs need only the math libraries, specified like this;
+#
+LIBS    = -lm $(LDFLAGS)
+#
+# The drawing programs may also need access to the graphics libraries. This is
+# specified with the DLIBS variable.
+DLIBS  = $(LIBS)
+#
+# ----------------------------------------------------------------------------
+#  (After this point there should not be any reason to change anything)
+# ----------------------------------------------------------------------------
+#
+#
+# the list of programs
+# draw programs are listed last since they are the most likely to cause
+# compilation or linking problems
+
+PROGS   =		clique \
+				consense \
+				contml \
+				contrast \
+				dnacomp \
+				dnadist \
+				dnainvar \
+				dnaml \
+				dnamlk \
+				dnamove \
+				dnapars \
+				dnapenny \
+				dolmove \
+				dollop \
+				dolpenny \
+				factor \
+				fitch \
+				gendist \
+				kitsch \
+				mix \
+				move \
+				neighbor \
+				pars \
+				penny \
+				proml \
+				promlk \
+				protdist \
+				protpars \
+				restdist \
+				restml \
+				retree \
+				seqboot \
+				treedist \
+        		drawgram \
+				drawtree 
+							
+DYLIBS  =       libdrawgram.so \
+		        libdrawtree.so
+
+JARS    =       javajars/DrawGram.jar \
+                javajars/DrawTree.jar \
+                javajars/DrawGramJava.unx\
+                javajars/DrawTreeJava.unx
+#
+# general commands
+#
+
+#  The first target it executed if you just type "make".  It tells you how to
+#  use the Makefile.
+#
+help:
+	@echo ""
+	@echo " To use the PHYLIP v3.6 Makefile, type"
+	@echo "     make install       to compile the whole package and install"
+	@echo "                          the executables in $(EXEDIR), and then"
+	@echo "                          remove the object files to save space"
+	@echo "     make all           to compile the whole package but not install it"
+	@echo "                          or remove the object files"
+	@echo "     make put           to move the executables into $(EXEDIR)"
+	@echo "     make clean         to remove all object files and executables from the"
+	@echo "                          current directory"
+	@echo "     make dnaml         to compile and link one program, (in this example,"
+	@echo "                          Dnaml) and leave the executable and object files"
+	@echo "                          in the current directory (where the source code is)."
+	@echo "                          You will have to move the executable into the"
+	@echo "                          executables directory (e.g. \"mv dnaml $(EXEDIR)\")"
+	@echo "                          Note that the program name should be lower case."
+	@echo " "
+
+introduce:
+	@echo "Building PHYLIP version $(VERSION)"
+
+all:        introduce $(PROGS) $(DYLIBS)
+	@echo "Finished compiling."
+	@echo ""
+
+install:        all put clean
+	@echo "Done."
+	@echo ""
+
+put:
+	@echo "Installing PHYLIP v3.6 binaries in $(EXEDIR)"
+	@mkdir -p $(EXEDIR)
+	@cp $(PROGS) $(EXEDIR)
+	@echo "Installing dynamic libraries in $(EXEDIR)"
+	@cp $(DYLIBS) $(EXEDIR)
+	@echo "Installing jar files in $(EXEDIR)"
+	@cp $(JARS) $(EXEDIR)
+	@echo "Installing font files in $(DATADIR)"
+	@mkdir -p $(DATADIR)
+	@cp font* $(DATADIR)
+	@cd $(DATADIR) && ln -s font1 fontfile
+	@echo "Finished installation."
+	@echo ""
+
+clean:
+	@echo "Removing object files to save space"
+	@rm -f *.o
+	@echo "Finished removing object files.  Now will remove"
+	@echo "executable files from the current directory, but not from the"
+	@echo "executables directory.  (If some are not here, the makefile"
+	@echo "will terminate with an error message but this is not a problem)"
+	@echo ""
+	@echo "Removing executables from this directory"
+	@rm -f $(PROGS)
+	@echo "Finished cleanup."
+	@echo ""
+
+distclean: clean
+	@echo "Removing executables"
+	@rm -rf $(EXEDIR)/* $(DATADIR)/*
+	@echo "Finaly removed all executable files."
+	@echo ""
+
+#
+# compile object files shared between programs
+# (make's implicit rule for %.o will take care of these)
+#
+
+phylip.o:     phylip.h
+seq.o:        phylip.h seq.h
+disc.o:       phylip.h disc.h
+discrete.o:   phylip.h discrete.h
+dollo.o:      phylip.h dollo.h
+wagner.o:     phylip.h wagner.h
+dist.o:       phylip.h dist.h
+cont.o:       phylip.h cont.h
+mlclock.o:    phylip.h mlclock.h
+moves.o:      phylip.h moves.h
+printree.o:   phylip.h printree.h
+
+#
+# compile the individual programs
+#
+
+clique.o:       clique.c disc.h phylip.h
+
+clique:         clique.o disc.o phylip.o
+	$(CC) $(CFLAGS) clique.o disc.o phylip.o $(LIBS) -o clique
+
+cons.o:         cons.c cons.h phylip.h 
+
+consense.o:     consense.c cons.h phylip.h
+
+consense:       consense.o phylip.o cons.o
+	$(CC) $(CFLAGS) consense.o phylip.o cons.o $(LIBS) -o consense
+
+contml.o:       contml.c cont.h phylip.h
+
+contml:       contml.o cont.o phylip.o
+	$(CC) $(CFLAGS) contml.o cont.o phylip.o $(LIBS) -o contml
+
+contrast.o:       contrast.c cont.h phylip.h
+
+contrast:       contrast.o cont.o phylip.o
+	$(CC) $(CFLAGS) contrast.o cont.o phylip.o $(LIBS) -o contrast
+
+dnacomp.o:      dnacomp.c seq.h phylip.h
+
+dnacomp:      dnacomp.o seq.o phylip.o
+	$(CC) $(CFLAGS) dnacomp.o seq.o phylip.o $(LIBS) -o dnacomp
+
+dnadist.o:      dnadist.c seq.h phylip.h
+
+dnadist:      dnadist.o seq.o phylip.o
+	$(CC) $(CFLAGS) dnadist.o seq.o phylip.o $(LIBS) -o dnadist
+
+dnainvar.o:      dnainvar.c seq.h phylip.h
+
+dnainvar:      dnainvar.o seq.o phylip.o
+	$(CC) $(CFLAGS) dnainvar.o seq.o phylip.o $(LIBS) -o dnainvar
+
+dnaml.o:      dnaml.c seq.h phylip.h
+
+dnaml:      dnaml.o seq.o phylip.o
+	$(CC) $(CFLAGS) dnaml.o seq.o phylip.o $(LIBS) -o dnaml
+
+dnamlk.o:      dnamlk.c seq.h phylip.h mlclock.h printree.h
+
+dnamlk:      dnamlk.o seq.o phylip.o mlclock.o printree.o
+	$(CC) $(CFLAGS) dnamlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o dnamlk
+
+dnamove.o:      dnamove.c seq.h moves.h phylip.h
+
+dnamove:      dnamove.o seq.o moves.o phylip.o
+	$(CC) $(CFLAGS) dnamove.o seq.o moves.o phylip.o $(LIBS) -o dnamove
+
+dnapenny.o:      dnapenny.c seq.h phylip.h
+
+dnapenny:      dnapenny.o seq.o phylip.o
+	$(CC) $(CFLAGS) dnapenny.o seq.o phylip.o $(LIBS) -o dnapenny
+
+dnapars.o:      dnapars.c seq.h phylip.h
+
+dnapars:      dnapars.o seq.o phylip.o
+	$(CC) $(CFLAGS) dnapars.o seq.o phylip.o $(LIBS) -o dnapars
+
+dolmove.o:       dolmove.c disc.h moves.h dollo.h phylip.h
+
+dolmove:       dolmove.o disc.o moves.o dollo.o phylip.o
+	$(CC) $(CFLAGS) dolmove.o disc.o moves.o dollo.o phylip.o $(LIBS) -o dolmove
+
+dollop.o:       dollop.c disc.h dollo.h phylip.h
+
+dollop:       dollop.o disc.o dollo.o phylip.o
+	$(CC) $(CFLAGS) dollop.o disc.o dollo.o phylip.o $(LIBS) -o dollop
+
+dolpenny.o:       dolpenny.c disc.h dollo.h phylip.h
+
+dolpenny:       dolpenny.o disc.o dollo.o phylip.o
+	$(CC) $(CFLAGS) dolpenny.o disc.o dollo.o phylip.o $(LIBS) -o dolpenny
+
+draw.o:   draw.c draw.h phylip.h 
+	$(CC) $(DFLAGS) -c draw.c
+
+draw2.o:   draw2.c draw.h phylip.h 
+	$(CC) $(DFLAGS) -c draw2.c
+
+drawgram.o:     drawgram.c draw.h phylip.h
+	$(CC) $(DFLAGS) -c drawgram.c
+
+drawgram:     drawgram.o draw.o draw2.o phylip.o
+	$(CC) $(DFLAGS) draw.o draw2.o drawgram.o phylip.o $(DLIBS) -o drawgram
+	
+# needed by java	
+libdrawgram.so:   drawgram.o draw.o draw2.o phylip.o
+	$(CC) $(CFLAGS) -o libdrawgram.so -shared -fPIC drawgram.c draw.c draw2.c phylip.c $(CLIBS) $(LDFLAGS)
+
+drawtree.o:     drawtree.c draw.h phylip.h
+	$(CC) $(DFLAGS)  -shared -fPIC -c drawtree.c
+
+drawtree:     drawtree.o draw.o draw2.o phylip.o
+	$(CC) $(DFLAGS) draw.o draw2.o drawtree.o phylip.o $(DLIBS) -o drawtree
+
+# needed by java	
+libdrawtree.so:     drawtree.o draw.o draw2.o phylip.o
+	$(CC) $(CFLAGS) -o libdrawtree.so  -shared -fPIC drawtree.c draw.c draw2.c phylip.c $(CLIBS) $(LDFLAGS)
+
+factor.o:       factor.c phylip.h
+
+factor:       factor.o phylip.o
+	$(CC) $(CFLAGS) factor.o phylip.o $(LIBS) -o factor
+
+fitch.o:        fitch.c dist.h phylip.h
+
+fitch:        fitch.o dist.o phylip.o
+	$(CC) $(CFLAGS) fitch.o dist.o phylip.o $(LIBS) -o fitch
+
+gendist.o:      gendist.c phylip.h
+
+gendist:      gendist.o phylip.o
+	$(CC) $(CFLAGS) gendist.o phylip.o $(LIBS) -o gendist
+
+kitsch.o:        kitsch.c dist.h phylip.h
+
+kitsch:        kitsch.o dist.o phylip.o
+	$(CC) $(CFLAGS) kitsch.o dist.o phylip.o $(LIBS) -o kitsch
+
+mix.o:        mix.c disc.h wagner.h phylip.h
+
+mix:        mix.o disc.o wagner.o phylip.o
+	$(CC) $(CFLAGS) mix.o disc.o wagner.o phylip.o $(LIBS) -o mix
+
+move.o:        move.c disc.h moves.h wagner.h phylip.h
+
+move:        move.o disc.o moves.o wagner.o phylip.o
+	$(CC) $(CFLAGS) move.o disc.o moves.o wagner.o phylip.o $(LIBS) -o move
+
+neighbor.o:        neighbor.c dist.h phylip.h
+
+neighbor:        neighbor.o dist.o phylip.o
+	$(CC) $(CFLAGS) neighbor.o dist.o phylip.o $(LIBS) -o neighbor
+
+pars.o:   pars.c discrete.h phylip.h
+
+pars: pars.o discrete.o phylip.o
+	$(CC) $(CFLAGS) pars.o discrete.o phylip.o $(LIBS) -o pars
+
+penny.o:  penny.c disc.h wagner.h phylip.h
+
+penny:  penny.o disc.o wagner.o phylip.o
+	$(CC) $(CFLAGS) penny.o disc.o wagner.o  phylip.o $(LIBS) -o penny
+
+proml.o:      proml.c seq.h phylip.h
+
+proml:      proml.o seq.o phylip.o
+	$(CC) $(CFLAGS) proml.o seq.o phylip.o $(LIBS) -o proml
+
+promlk.o:      promlk.c seq.h phylip.h mlclock.h printree.h
+
+promlk:      promlk.o seq.o phylip.o mlclock.o printree.o
+	$(CC) $(CFLAGS) promlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o promlk
+
+protdist.o:      protdist.c seq.h phylip.h
+
+protdist:      protdist.o seq.o phylip.o
+	$(CC) $(CFLAGS) protdist.o seq.o phylip.o $(LIBS) -o protdist
+
+protpars.o: protpars.c seq.h phylip.h
+
+protpars: protpars.o seq.o phylip.o
+	$(CC) $(CFLAGS) protpars.o seq.o phylip.o $(LIBS) -o protpars
+
+restdist.o: restdist.c seq.h phylip.h
+
+restdist: restdist.o seq.o phylip.o
+	$(CC) $(CFLAGS) restdist.o seq.o phylip.o $(LIBS) -o restdist
+
+restml.o: restml.c seq.h phylip.h
+
+restml: restml.o seq.o phylip.o
+	$(CC) $(CFLAGS) restml.o seq.o phylip.o $(LIBS) -o restml
+
+retree.o:       retree.c moves.h phylip.h
+
+retree:       retree.o moves.o phylip.o
+	$(CC) $(CFLAGS) retree.o moves.o phylip.o $(LIBS) -o retree
+
+seqboot.o:      seqboot.c phylip.h
+
+seqboot:      seqboot.o seq.o phylip.o
+	$(CC) $(CFLAGS) seqboot.o seq.o phylip.o $(LIBS) -o seqboot
+
+treedist.o:     treedist.c cons.h phylip.h
+
+treedist:     treedist.o phylip.o cons.o
+	$(CC) $(CFLAGS) treedist.o cons.o phylip.o $(LIBS) -o treedist
+
+
+# ----------------------------------------------------------------------------
+#  The following section is used to build a PHYLIP distribution. All sources
+#  and other files except the documentation files must be placed in the
+#  current directory.  The HTML documentation files must be in folder "doc"
+#  within this, the Mac icons in folder "mac", and the Windows icons and
+#  resource files must be in folder "icons"
+#
+#  Usage:
+#  	make distdir	- Build the distribution dir phylip-<vers>/
+#  	make dist	- Make a tarred and gzipped phylip-<vers>.tar.gz
+# ----------------------------------------------------------------------------
+
+DIST_COMMON = phylip.html 
+
+DOCS= doc/clique.html doc/consense.html doc/contchar.html doc/contml.html \
+      doc/contrast.html doc/discrete.html doc/distance.html doc/dnacomp.html \
+      doc/dnadist.html doc/dnainvar.html doc/dnaml.html doc/dnamlk.html \
+      doc/dnamove.html doc/dnapars.html doc/dnapenny.html doc/dollop.html \
+      doc/dolmove.html doc/dolpenny.html doc/drawgram.html doc/draw.html \
+      doc/drawtree.html doc/factor.html doc/fitch.html doc/gendist.html \
+      doc/kitsch.html doc/main.html doc/mix.html doc/move.html \
+      doc/neighbor.html doc/pars.html doc/penny.html doc/proml.html \
+      doc/promlk.html doc/protdist.html doc/protpars.html doc/restdist.html \
+      doc/restml.html doc/retree.html doc/seqboot.html doc/sequence.html \
+      doc/treedist.html doc/phylip.gif
+
+SOURCES= COPYRIGHT Makefile Makefile.cyg Makefile.osx Makefile.unx linkmac  \
+     clique.c cons.c consense.c cons.h cont.c \
+     cont.h contml.c contrast.c disc.c disc.h discrete.c discrete.h dist.c \
+	 dist.h dnacomp.c dnadist.c dnainvar.c dnaml.c dnamlk.c dnamove.c \
+	 dnapars.c dnapenny.c dollo.c dollo.h dollop.c dolmove.c dolpenny.c \
+	 draw2.c draw.c drawgram.c draw.h drawtree.c \
+	 factor.c fitch.c gendist.c \
+	 kitsch.c mix.c move.c \
+	 moves.c moves.h neighbor.c pars.c penny.c \
+	 phylip.c phylip.h proml.c promlk.c protdist.c protpars.c restdist.c \
+	 restml.c retree.c seqboot.c seq.c seq.h treedist.c wagner.c wagner.h \
+	 mlclock.c mlclock.h printree.c printree.h
+
+MAC= \
+		Info.plist.in boot.icns clique.icns command.in consense.icns \
+	contml.icns contrast.icns disc.icns dist.icns dna.icns dnacomp.icns \
+	dnadist.icns dnainvar.icns dnaml.icns dnamlk.icns dnamove.icns \
+	dnapars.icns dnapenny.icns dollo.icns dollop.icns dolmove.icns \
+	dolpenny.icns drawgram.icns drawtree.icns factor.icns fitch.icns \
+	gendist.icns kitsch.icns mac.sit mix.icns move.icns neighbor.icns \
+	pars.icns penny.icns proml.icns promlk.icns protdist.icns protein.icns \
+	protpars.icns restdist.icns restml.icns restrict.icns retree.icns \
+	seqboot.icns treedist.icns
+
+ICONS= 		boot.ico clique.ico clique.rc clique.rcb consense.ico \
+		consense.rc consense.rcb contml.ico contml.rc contml.rcb \
+		contrast.ico contrast.rc contrast.rcb disc.ico dist.ico dna.ico \
+		dnacomp.rc dnacomp.rcb dnadist.rc dnadist.rcb dnainvar.rc \
+		dnainvar.rcb dnaml.rc dnaml.rcb dnamlk.rc dnamlk.rcb dnamove.rc \
+		dnamove.rcb dnapars.rc dnapars.rcb dnapenny.rc dnapenny.rcb \
+		dollo.ico dollop.rc dollop.rcb dolmove.rc dolmove.rcb \
+		dolpenny.rc dolpenny.rcb drawgram.ico drawgram.rc drawgram.rcb \
+		drawtree.ico drawtree.rc drawtree.rcb factor.rc factor.rcb \
+		fitch.rc fitch.rcb gendist.ico gendist.rc gendist.rcb kitsch.rc \
+		kitsch.rcb mix.rc mix.rcb move.rc move.rcb neighbor.rc \
+		neighbor.rcb pars.rc pars.rcb penny.rc penny.rcb proml.rc \
+		proml.rcb promlk.rc promlk.rcb protdist.rc protdist.rcb \
+		protein.ico protpars.rc protpars.rcb restdist.rc restdist.rcb \
+		restml.rc restml.rcb restrict.ico retree.ico retree.rc \
+		retree.rcb seqboot.rc seqboot.rcb treedist.ico treedist.rc \
+		treedist.rcb
+
+FONTS= font1 font2 font3 font4 font5 font6
+
+TESTDIR=   clique consense contml contrast dnacomp \
+      dnadist dnainvar dnaml dnamlk dnamove dnapars dnapenny dollop \
+      dolmove dolpenny drawgram drawtree factor fitch gendist \
+      kitsch mix move neighbor pars penny proml promlk \
+      protdist protpars restdist restml retree seqboot  treedist
+      
+JARAJAR=    javajars/DrawGram.jar javajars/DrawTree.jar \
+        javajars/DrawGramJava.bat javajars/DrawTreeJava.bat \
+        javajars/DrawGramJava.exe javajars/DrawTreeJava.exe \
+        javajars/DrawGramJava.unx javajars/DrawTreeJava.unx
+ 
+DISTDIR=$(PACKAGE)-$(VERSION)
+dist_SRCDIR=$(DISTDIR)/src
+dist_DOCDIR=$(DISTDIR)/doc
+dist_EXEDIR=$(DISTDIR)/exe
+dist_JAVADIR=$(DISTDIR)/src/javajars
+MACICONDIR=src/mac
+
+SHELL=bash
+
+# We use this target to create a tarred and gzipped distribution of PHYLIP
+dist: distdir
+	-chmod -R a+r $(DISTDIR)
+	tar chozf $(DISTDIR).tar.gz $(DISTDIR)
+	-rm -rf $(DISTDIR)
+
+# This target creates the distribution directory
+distdir: $(DIST_COMMON) $(DOCS) $(SOURCES)
+	-rm -rf $(DISTDIR)
+	mkdir $(DISTDIR) && \
+	mkdir $(dist_EXEDIR) && \
+	mkdir $(dist_DOCDIR) && \
+	mkdir $(dist_SRCDIR) && \
+	mkdir $(dist_JAVADIR)
+	mkdir $(dist_SRCDIR)/mac
+	mkdir $(dist_SRCDIR)/icons
+	mkdir $(dist_EXEDIR)/testdata
+	for i in $(TESTDIR); do \
+      mkdir $(dist_EXEDIR)/testdata/$$i; \
+      cp TestData/$$i/*.txt $(dist_EXEDIR)/testdata/$$i; \
+    done
+	for i in $(DIST_COMMON) ; do \
+	  cp -r $$i $(DISTDIR) ; \
+	done
+	for i in $(DOCS) ; do \
+	  cp -r $$i $(dist_DOCDIR) ; \
+	done
+	for i in $(SOURCES) ; do \
+	  cp -r $$i $(dist_SRCDIR) ; \
+	done
+	for i in $(MAC) ; do \
+	  cp -r mac/$$i $(dist_SRCDIR)/mac ; \
+	done
+	for i in $(ICONS) ; do \
+	  cp -r icons/$$i $(dist_SRCDIR)/icons ; \
+	done
+	for i in $(FONTS) ; do \
+	  cp -r $$i $(dist_SRCDIR) ; \
+	done
+	for i in $(JARAJAR) ; do \
+	  cp $$i $(dist_JAVADIR) ; \
+	done
+
+# This target untars the dist and checks that it can be compiled and remade
+distcheck: dist
+	-rm -rf $(DISTDIR)
+	tar xzf $(DISTDIR).tar.gz
+	cd $(DISTDIR)/$(SRCDIR) \
+	  && make all
+	-rm -rf $(DISTDIR)
+	@echo "$(DISTDIR).tar.gz is ready for distribution"
+
+# Makefile

=== modified file '.pc/hardening.patch/src/Makefile.unx' (properties changed: +x to -x)
--- .pc/hardening.patch/src/Makefile.unx	2013-08-07 22:17:03 +0000
+++ .pc/hardening.patch/src/Makefile.unx	2015-04-04 21:58:41 +0000
@@ -1,9 +1,9 @@
 # Makefile
 #
-# Unix Makefile for PHYLIP 3.695
+# Unix Makefile for PHYLIP 3.696
 
 PACKAGE=phylip
-VERSION=3.695
+VERSION=3.696
 
 # We use GNU's version of the make utility. It may be called "gmake" on
 # your system.
@@ -20,11 +20,11 @@
 # When uncompressed and extracted, the tar archive phylip-3.6x.tar.gz 
 # produces the following directory structure:
 #
-#   phylip-3.6x/source -- the source code, including this Makefile
+#   phylip-3.6x/src -- the source code, including this Makefile
 #   phylip-3.6x/exe -- executables, changed by changing $(EXEDIR) value
 #   phylip-3.6x/doc -- html documentation
 #
-#  To use the PHYLIP v3.6 Makefile, type from the phylip-3.6x/source directory:
+#  To use the PHYLIP v3.6 Makefile, type from the phylip-3.6x/src directory:
 #
 #      make install         to compile the whole package and install
 #                           the executables in $(EXEDIR), and then
@@ -92,10 +92,10 @@
 #
 #
 #A minimal one
-#CFLAGS =
+CFLAGS =
 #
 # A basic one for debugging
-CFLAGS  = -g 
+#CFLAGS  = -g 
 #
 # An optimized one for gcc
 #CFLAGS  = -O3 -DUNX -fomit-frame-pointer
@@ -180,17 +180,10 @@
 DYLIBS  =       libdrawgram.so \
 		        libdrawtree.so
 
-JARS	=	javajars/DrawGram.jar \
+JARS    =       javajars/DrawGram.jar \
                 javajars/DrawTree.jar \
                 javajars/DrawGramJava.unx\
                 javajars/DrawTreeJava.unx
-
-TESTDIR	=   	clique consense contml contrast dnacomp \
-      dnadist dnainvar dnaml dnamlk dnamove dnapars dnapenny dollop \
-      dolmove dolpenny drawgram drawtree factor fitch gendist \
-      kitsch mix move neighbor pars penny proml promlk \
-      protdist protpars restdist restml retree seqboot  treedist
-
 #
 # general commands
 #
@@ -229,7 +222,7 @@
 	@echo ""
 
 put:
-	@echo "Installing PHYLIP v$(VERSION) binaries in $(EXEDIR)"
+	@echo "Installing PHYLIP v3.6 binaries in $(EXEDIR)"
 	@mkdir -p $(EXEDIR)
 	@cp $(PROGS) $(EXEDIR)
 	@echo "Installing dynamic libraries in $(EXEDIR)"
@@ -240,12 +233,6 @@
 	@mkdir -p $(DATADIR)
 	@cp font* $(DATADIR)
 	@cd $(DATADIR) && ln -s font1 fontfile
-	@echo "Copying testdata files to $(EXEDIR)/testdata/..."
-	mkdir $(EXEDIR)/testdata
-	for i in $(TESTDIR); do \
-      	  mkdir $(EXEDIR)/testdata/$$i; \
-      	  cp testdata/$$i/*.txt $(EXEDIR)/testdata/$$i; \
-    	done
 	@echo "Finished installation."
 	@echo ""
 
@@ -264,7 +251,7 @@
 
 distclean: clean
 	@echo "Removing executables"
-	@rm -rf $(EXEDIR) $(DATADIR)
+	@rm -rf $(EXEDIR)/* $(DATADIR)/*
 	@echo "Finaly removed all executable files."
 	@echo ""
 
@@ -495,39 +482,29 @@
 #  	make dist	- Make a tarred and gzipped phylip-<vers>.tar.gz
 # ----------------------------------------------------------------------------
 
-DIST_COMMON = ../phylip.html 
-
-DOC_DIR = ../doc
-
-IMG_DIR = ../doc/images
-
-TEST_DIR = ../src/testdata
-
-DOCS= clique.html consense.html contchar.html contml.html \
-      contrast.html discrete.html distance.html dnacomp.html \
-      dnadist.html dnainvar.html dnaml.html dnamlk.html \
-      dnamove.html dnapars.html dnapenny.html dollop.html \
-      dolmove.html dolpenny.html drawgram.html draw.html \
-      drawtree.html factor.html fitch.html gendist.html \
-      kitsch.html main.html mix.html move.html \
-      neighbor.html pars.html penny.html proml.html \
-      promlk.html protdist.html protpars.html restdist.html \
-      restml.html retree.html seqboot.html sequence.html \
-      treedist.html phylip.gif
-      
-IMAGES= DrawGramCat.png DrawGramControls.png \
-     DrawTreeCat.png DrawTreeControls.png \
-     InputTree.png
-
-SOURCES= COPYRIGHT Makefile.cyg Makefile.osx Makefile.unx linkmac  \
+DIST_COMMON = phylip.html 
+
+DOCS= doc/clique.html doc/consense.html doc/contchar.html doc/contml.html \
+      doc/contrast.html doc/discrete.html doc/distance.html doc/dnacomp.html \
+      doc/dnadist.html doc/dnainvar.html doc/dnaml.html doc/dnamlk.html \
+      doc/dnamove.html doc/dnapars.html doc/dnapenny.html doc/dollop.html \
+      doc/dolmove.html doc/dolpenny.html doc/drawgram.html doc/draw.html \
+      doc/drawtree.html doc/factor.html doc/fitch.html doc/gendist.html \
+      doc/kitsch.html doc/main.html doc/mix.html doc/move.html \
+      doc/neighbor.html doc/pars.html doc/penny.html doc/proml.html \
+      doc/promlk.html doc/protdist.html doc/protpars.html doc/restdist.html \
+      doc/restml.html doc/retree.html doc/seqboot.html doc/sequence.html \
+      doc/treedist.html doc/phylip.gif
+
+SOURCES= COPYRIGHT Makefile Makefile.cyg Makefile.osx Makefile.unx linkmac  \
      clique.c cons.c consense.c cons.h cont.c \
      cont.h contml.c contrast.c disc.c disc.h discrete.c discrete.h dist.c \
 	 dist.h dnacomp.c dnadist.c dnainvar.c dnaml.c dnamlk.c dnamove.c \
 	 dnapars.c dnapenny.c dollo.c dollo.h dollop.c dolmove.c dolpenny.c \
 	 draw2.c draw.c drawgram.c draw.h drawtree.c \
 	 factor.c fitch.c gendist.c \
-	 interface.c interface.h io.h kitsch.c macface.c macface.h mix.c move.c \
-	 moves.c moves.h neighbor.c newmove.c pars.c penny.c \
+	 kitsch.c mix.c move.c \
+	 moves.c moves.h neighbor.c pars.c penny.c \
 	 phylip.c phylip.h proml.c promlk.c protdist.c protpars.c restdist.c \
 	 restml.c retree.c seqboot.c seq.c seq.h treedist.c wagner.c wagner.h \
 	 mlclock.c mlclock.h printree.c printree.h
@@ -562,6 +539,12 @@
 		treedist.rcb
 
 FONTS= font1 font2 font3 font4 font5 font6
+
+TESTDIR=   clique consense contml contrast dnacomp \
+      dnadist dnainvar dnaml dnamlk dnamove dnapars dnapenny dollop \
+      dolmove dolpenny drawgram drawtree factor fitch gendist \
+      kitsch mix move neighbor pars penny proml promlk \
+      protdist protpars restdist restml retree seqboot  treedist
       
 JARAJAR=    javajars/DrawGram.jar javajars/DrawTree.jar \
         javajars/DrawGramJava.bat javajars/DrawTreeJava.bat \
@@ -571,7 +554,6 @@
 DISTDIR=$(PACKAGE)-$(VERSION)
 dist_SRCDIR=$(DISTDIR)/src
 dist_DOCDIR=$(DISTDIR)/doc
-dist_IMGDIR=$(DISTDIR)/doc/images
 dist_EXEDIR=$(DISTDIR)/exe
 dist_JAVADIR=$(DISTDIR)/src/javajars
 MACICONDIR=src/mac
@@ -585,33 +567,29 @@
 	-rm -rf $(DISTDIR)
 
 # This target creates the distribution directory
-distdir: $(DIST_COMMON) $(SOURCES) $(TESTDIR) $(JAVAJAR) $(DYLIBS)
+distdir: $(DIST_COMMON) $(DOCS) $(SOURCES)
 	-rm -rf $(DISTDIR)
-	mkdir $(DISTDIR)
-	mkdir $(dist_EXEDIR)
-	mkdir $(dist_DOCDIR)
-	mkdir $(dist_IMGDIR)
-	mkdir $(dist_SRCDIR)
+	mkdir $(DISTDIR) && \
+	mkdir $(dist_EXEDIR) && \
+	mkdir $(dist_DOCDIR) && \
+	mkdir $(dist_SRCDIR) && \
 	mkdir $(dist_JAVADIR)
 	mkdir $(dist_SRCDIR)/mac
 	mkdir $(dist_SRCDIR)/icons
-	mkdir $(dist_SRCDIR)/testdata
+	mkdir $(dist_EXEDIR)/testdata
 	for i in $(TESTDIR); do \
-      	  mkdir $(dist_SRCDIR)/testdata/$$i; \
-      	  cp $(TEST_DIR)/$$i/*.txt $(dist_SRCDIR)/testdata/$$i; \
-    	done
+      mkdir $(dist_EXEDIR)/testdata/$$i; \
+      cp TestData/$$i/*.txt $(dist_EXEDIR)/testdata/$$i; \
+    done
 	for i in $(DIST_COMMON) ; do \
 	  cp -r $$i $(DISTDIR) ; \
 	done
+	for i in $(DOCS) ; do \
+	  cp -r $$i $(dist_DOCDIR) ; \
+	done
 	for i in $(SOURCES) ; do \
 	  cp -r $$i $(dist_SRCDIR) ; \
 	done
-	for i in $(DOCS) ; do \
-	  cp -r $(DOC_DIR)/$$i $(dist_DOCDIR) ; \
-	done
-	for i in $(IMAGES) ; do \
-	  cp -r $(IMG_DIR)/$$i $(dist_IMGDIR) ; \
-	done
 	for i in $(MAC) ; do \
 	  cp -r mac/$$i $(dist_SRCDIR)/mac ; \
 	done
@@ -625,10 +603,6 @@
 	  cp $$i $(dist_JAVADIR) ; \
 	done
 
-disttest:
-	cd phylip-3.695/src; \
-	ls
-
 # This target untars the dist and checks that it can be compiled and remade
 distcheck: dist
 	-rm -rf $(DISTDIR)

=== modified file '.pc/install_fonts_data.patch/src/Makefile.unx' (properties changed: +x to -x)
--- .pc/install_fonts_data.patch/src/Makefile.unx	2013-08-07 22:17:03 +0000
+++ .pc/install_fonts_data.patch/src/Makefile.unx	2015-04-04 21:58:41 +0000
@@ -1,9 +1,9 @@
 # Makefile
 #
-# Unix Makefile for PHYLIP 3.695
+# Unix Makefile for PHYLIP 3.696
 
 PACKAGE=phylip
-VERSION=3.695
+VERSION=3.696
 
 # We use GNU's version of the make utility. It may be called "gmake" on
 # your system.
@@ -20,11 +20,11 @@
 # When uncompressed and extracted, the tar archive phylip-3.6x.tar.gz 
 # produces the following directory structure:
 #
-#   phylip-3.6x/source -- the source code, including this Makefile
+#   phylip-3.6x/src -- the source code, including this Makefile
 #   phylip-3.6x/exe -- executables, changed by changing $(EXEDIR) value
 #   phylip-3.6x/doc -- html documentation
 #
-#  To use the PHYLIP v3.6 Makefile, type from the phylip-3.6x/source directory:
+#  To use the PHYLIP v3.6 Makefile, type from the phylip-3.6x/src directory:
 #
 #      make install         to compile the whole package and install
 #                           the executables in $(EXEDIR), and then
@@ -91,10 +91,10 @@
 #
 #
 #A minimal one
-#CFLAGS =
+CFLAGS =
 #
 # A basic one for debugging
-CFLAGS  = -g 
+#CFLAGS  = -g 
 #
 # An optimized one for gcc
 #CFLAGS  = -O3 -DUNX -fomit-frame-pointer
@@ -179,17 +179,10 @@
 DYLIBS  =       libdrawgram.so \
 		        libdrawtree.so
 
-JARS	=	javajars/DrawGram.jar \
+JARS    =       javajars/DrawGram.jar \
                 javajars/DrawTree.jar \
                 javajars/DrawGramJava.unx\
                 javajars/DrawTreeJava.unx
-
-TESTDIR	=   	clique consense contml contrast dnacomp \
-      dnadist dnainvar dnaml dnamlk dnamove dnapars dnapenny dollop \
-      dolmove dolpenny drawgram drawtree factor fitch gendist \
-      kitsch mix move neighbor pars penny proml promlk \
-      protdist protpars restdist restml retree seqboot  treedist
-
 #
 # general commands
 #
@@ -228,7 +221,7 @@
 	@echo ""
 
 put:
-	@echo "Installing PHYLIP v$(VERSION) binaries in $(EXEDIR)"
+	@echo "Installing PHYLIP v3.6 binaries in $(EXEDIR)"
 	@mkdir -p $(EXEDIR)
 	@cp $(PROGS) $(EXEDIR)
 	@echo "Installing dynamic libraries in $(EXEDIR)"
@@ -237,12 +230,6 @@
 	@cp $(JARS) $(EXEDIR)
 	@echo "Installing font files in $(EXEDIR)"
 	@cp font* $(EXEDIR)
-	@echo "Copying testdata files to $(EXEDIR)/testdata/..."
-	mkdir $(EXEDIR)/testdata
-	for i in $(TESTDIR); do \
-      	  mkdir $(EXEDIR)/testdata/$$i; \
-      	  cp testdata/$$i/*.txt $(EXEDIR)/testdata/$$i; \
-    	done
 	@echo "Finished installation."
 	@echo ""
 
@@ -486,39 +473,29 @@
 #  	make dist	- Make a tarred and gzipped phylip-<vers>.tar.gz
 # ----------------------------------------------------------------------------
 
-DIST_COMMON = ../phylip.html 
-
-DOC_DIR = ../doc
-
-IMG_DIR = ../doc/images
-
-TEST_DIR = ../src/testdata
-
-DOCS= clique.html consense.html contchar.html contml.html \
-      contrast.html discrete.html distance.html dnacomp.html \
-      dnadist.html dnainvar.html dnaml.html dnamlk.html \
-      dnamove.html dnapars.html dnapenny.html dollop.html \
-      dolmove.html dolpenny.html drawgram.html draw.html \
-      drawtree.html factor.html fitch.html gendist.html \
-      kitsch.html main.html mix.html move.html \
-      neighbor.html pars.html penny.html proml.html \
-      promlk.html protdist.html protpars.html restdist.html \
-      restml.html retree.html seqboot.html sequence.html \
-      treedist.html phylip.gif
-      
-IMAGES= DrawGramCat.png DrawGramControls.png \
-     DrawTreeCat.png DrawTreeControls.png \
-     InputTree.png
-
-SOURCES= COPYRIGHT Makefile.cyg Makefile.osx Makefile.unx linkmac  \
+DIST_COMMON = phylip.html 
+
+DOCS= doc/clique.html doc/consense.html doc/contchar.html doc/contml.html \
+      doc/contrast.html doc/discrete.html doc/distance.html doc/dnacomp.html \
+      doc/dnadist.html doc/dnainvar.html doc/dnaml.html doc/dnamlk.html \
+      doc/dnamove.html doc/dnapars.html doc/dnapenny.html doc/dollop.html \
+      doc/dolmove.html doc/dolpenny.html doc/drawgram.html doc/draw.html \
+      doc/drawtree.html doc/factor.html doc/fitch.html doc/gendist.html \
+      doc/kitsch.html doc/main.html doc/mix.html doc/move.html \
+      doc/neighbor.html doc/pars.html doc/penny.html doc/proml.html \
+      doc/promlk.html doc/protdist.html doc/protpars.html doc/restdist.html \
+      doc/restml.html doc/retree.html doc/seqboot.html doc/sequence.html \
+      doc/treedist.html doc/phylip.gif
+
+SOURCES= COPYRIGHT Makefile Makefile.cyg Makefile.osx Makefile.unx linkmac  \
      clique.c cons.c consense.c cons.h cont.c \
      cont.h contml.c contrast.c disc.c disc.h discrete.c discrete.h dist.c \
 	 dist.h dnacomp.c dnadist.c dnainvar.c dnaml.c dnamlk.c dnamove.c \
 	 dnapars.c dnapenny.c dollo.c dollo.h dollop.c dolmove.c dolpenny.c \
 	 draw2.c draw.c drawgram.c draw.h drawtree.c \
 	 factor.c fitch.c gendist.c \
-	 interface.c interface.h io.h kitsch.c macface.c macface.h mix.c move.c \
-	 moves.c moves.h neighbor.c newmove.c pars.c penny.c \
+	 kitsch.c mix.c move.c \
+	 moves.c moves.h neighbor.c pars.c penny.c \
 	 phylip.c phylip.h proml.c promlk.c protdist.c protpars.c restdist.c \
 	 restml.c retree.c seqboot.c seq.c seq.h treedist.c wagner.c wagner.h \
 	 mlclock.c mlclock.h printree.c printree.h
@@ -553,6 +530,12 @@
 		treedist.rcb
 
 FONTS= font1 font2 font3 font4 font5 font6
+
+TESTDIR=   clique consense contml contrast dnacomp \
+      dnadist dnainvar dnaml dnamlk dnamove dnapars dnapenny dollop \
+      dolmove dolpenny drawgram drawtree factor fitch gendist \
+      kitsch mix move neighbor pars penny proml promlk \
+      protdist protpars restdist restml retree seqboot  treedist
       
 JARAJAR=    javajars/DrawGram.jar javajars/DrawTree.jar \
         javajars/DrawGramJava.bat javajars/DrawTreeJava.bat \
@@ -562,7 +545,6 @@
 DISTDIR=$(PACKAGE)-$(VERSION)
 dist_SRCDIR=$(DISTDIR)/src
 dist_DOCDIR=$(DISTDIR)/doc
-dist_IMGDIR=$(DISTDIR)/doc/images
 dist_EXEDIR=$(DISTDIR)/exe
 dist_JAVADIR=$(DISTDIR)/src/javajars
 MACICONDIR=src/mac
@@ -576,33 +558,29 @@
 	-rm -rf $(DISTDIR)
 
 # This target creates the distribution directory
-distdir: $(DIST_COMMON) $(SOURCES) $(TESTDIR) $(JAVAJAR) $(DYLIBS)
+distdir: $(DIST_COMMON) $(DOCS) $(SOURCES)
 	-rm -rf $(DISTDIR)
-	mkdir $(DISTDIR)
-	mkdir $(dist_EXEDIR)
-	mkdir $(dist_DOCDIR)
-	mkdir $(dist_IMGDIR)
-	mkdir $(dist_SRCDIR)
+	mkdir $(DISTDIR) && \
+	mkdir $(dist_EXEDIR) && \
+	mkdir $(dist_DOCDIR) && \
+	mkdir $(dist_SRCDIR) && \
 	mkdir $(dist_JAVADIR)
 	mkdir $(dist_SRCDIR)/mac
 	mkdir $(dist_SRCDIR)/icons
-	mkdir $(dist_SRCDIR)/testdata
+	mkdir $(dist_EXEDIR)/testdata
 	for i in $(TESTDIR); do \
-      	  mkdir $(dist_SRCDIR)/testdata/$$i; \
-      	  cp $(TEST_DIR)/$$i/*.txt $(dist_SRCDIR)/testdata/$$i; \
-    	done
+      mkdir $(dist_EXEDIR)/testdata/$$i; \
+      cp TestData/$$i/*.txt $(dist_EXEDIR)/testdata/$$i; \
+    done
 	for i in $(DIST_COMMON) ; do \
 	  cp -r $$i $(DISTDIR) ; \
 	done
+	for i in $(DOCS) ; do \
+	  cp -r $$i $(dist_DOCDIR) ; \
+	done
 	for i in $(SOURCES) ; do \
 	  cp -r $$i $(dist_SRCDIR) ; \
 	done
-	for i in $(DOCS) ; do \
-	  cp -r $(DOC_DIR)/$$i $(dist_DOCDIR) ; \
-	done
-	for i in $(IMAGES) ; do \
-	  cp -r $(IMG_DIR)/$$i $(dist_IMGDIR) ; \
-	done
 	for i in $(MAC) ; do \
 	  cp -r mac/$$i $(dist_SRCDIR)/mac ; \
 	done
@@ -616,10 +594,6 @@
 	  cp $$i $(dist_JAVADIR) ; \
 	done
 
-disttest:
-	cd phylip-3.695/src; \
-	ls
-
 # This target untars the dist and checks that it can be compiled and remade
 distcheck: dist
 	-rm -rf $(DISTDIR)

=== added directory '.pc/soname.patch'
=== added directory '.pc/soname.patch/src'
=== added file '.pc/soname.patch/src/Makefile.unx'
--- .pc/soname.patch/src/Makefile.unx	1970-01-01 00:00:00 +0000
+++ .pc/soname.patch/src/Makefile.unx	2015-04-04 21:58:41 +0000
@@ -0,0 +1,613 @@
+# Makefile
+#
+# Unix Makefile for PHYLIP 3.696
+
+PACKAGE=phylip
+VERSION=3.696
+
+# We use GNU's version of the make utility. It may be called "gmake" on
+# your system.
+#
+# If you're using a RedHat Linux system with default locations for 
+# gcc libraries, you probably don't need to change anything. You might
+# might change the first noncomment statement below to redefine $(EXEDIR)
+# if you'd like your executables installed in a different location than
+# our default.
+#
+# Users with systems that differ substantially from ours may need to set
+# the following variables: $(CC) $(CFLAGS) $(DFLAGS) $(LIBS) $(DLIBS)
+#
+# When uncompressed and extracted, the tar archive phylip-3.6x.tar.gz 
+# produces the following directory structure:
+#
+#   phylip-3.6x/src -- the source code, including this Makefile
+#   phylip-3.6x/exe -- executables, changed by changing $(EXEDIR) value
+#   phylip-3.6x/doc -- html documentation
+#
+#  To use the PHYLIP v3.6 Makefile, type from the phylip-3.6x/src directory:
+#
+#      make install         to compile the whole package and install
+#                           the executables in $(EXEDIR), and then
+#                           remove the object files to save space
+#
+#      make all             to compile the whole package but not install it
+#                           or remove the object files. 
+#
+#      make put             to move the executables into $(EXEDIR)
+#
+#      make clean           to remove all object files and executables from the
+#                           current directory
+#
+#      make dnaml           to compile and link one program, (in this example,
+#                           DnaML) and leave the executable and object files
+#                           in the current directory (where the source code is).
+#                           You will have to move the executable into the
+#                           executables directory (e.g. "mv dnaml ../exe")
+#                           Note that the program name should be lower case.
+# 
+# ----------------------------------------------------------------------------
+#  (Starting here is the section where you may want to change things)
+# ----------------------------------------------------------------------------
+#
+# the following specifies the directory where the executables will be placed
+EXEDIR  = ../exe
+DATADIR = ../exe
+#
+# ----------------------------------------------------------------------------
+#
+# The following statements set these variables:
+#
+#    CC     -- the name (and, optionally, location) of your C compiler
+#    CFLAGS -- compiler directives needed to compile most programs
+#    DFLAGS -- compiler directives needed to compile draw programs
+#    LIBS   -- non-default system libraries needed to compile most programs
+#    DLIBS  -- non-default system libraries needed to compile draw programs
+#
+# We've provided a set of possible values for each variable.
+#
+# The value used is the one without a "#" at the beginning of the line.
+#
+# To try an alternate value, make sure the one you want has no "#"
+# as its first character and that all other possibilities have "#" for
+# their first character.
+#
+# Advanced users may need to further edit one of the alternatives in
+# order to correctly compile on their system.
+#
+# ----------------------------------------------------------------------------
+#
+# The next two assignments are the invocations of the compiler
+#
+# This one specifies the "cc" C compiler
+#CC        = cc
+#
+#  To use GCC instead:
+CC        = gcc
+#
+# ----------------------------------------------------------------------------
+#
+# This is the CFLAGS statement. It specifies compiler behavior.
+#
+# Here are some possible CFLAGS statements:
+#
+#
+#A minimal one
+CFLAGS =
+#
+# A basic one for debugging
+#CFLAGS  = -g 
+#
+# An optimized one for gcc
+#CFLAGS  = -O3 -DUNX -fomit-frame-pointer
+#
+# For some serious debugging using Gnu gcc
+#
+#CFLAGS=-g -DUNX -Wall -Wmain -Wmissing-prototypes -Wreturn-type -Wstrict-prototypes  -Wunused -Werror -Wredundant-decls -Waggregate-return -Wcast-align -Wcomment
+#
+# For doing code coverage with gcov
+#
+#CFLAGS	=	-ggdb -DUNX -fprofile-arcs -ftest-coverage
+#CFLAGS	=	-pg -DUNX
+#
+# For Digital Alpha systems with Compaq Tru64 Unix
+# (however, be aware that this may cause floating-point problems in programs
+#  like Dnaml owing to not using IEEE floating point standards).
+#CFLAGS = -fast -DUNX
+#
+# ----------------------------------------------------------------------------
+#
+# This is the DFLAGS statement. It specifies compiler behavior for the
+# programs drawgram and drawtree. It adds additional information to
+# the $(CFLAGS) value if needed.
+#
+DFLAGS = $(CFLAGS)
+#
+# ----------------------------------------------------------------------------
+#
+# Most of the programs need only the math libraries, specified like this;
+#
+LIBS    = -lm $(LDFLAGS)
+#
+# The drawing programs may also need access to the graphics libraries. This is
+# specified with the DLIBS variable.
+DLIBS  = $(LIBS)
+#
+# ----------------------------------------------------------------------------
+#  (After this point there should not be any reason to change anything)
+# ----------------------------------------------------------------------------
+#
+#
+# the list of programs
+# draw programs are listed last since they are the most likely to cause
+# compilation or linking problems
+
+PROGS   =		clique \
+				consense \
+				contml \
+				contrast \
+				dnacomp \
+				dnadist \
+				dnainvar \
+				dnaml \
+				dnamlk \
+				dnamove \
+				dnapars \
+				dnapenny \
+				dolmove \
+				dollop \
+				dolpenny \
+				factor \
+				fitch \
+				gendist \
+				kitsch \
+				mix \
+				move \
+				neighbor \
+				pars \
+				penny \
+				proml \
+				promlk \
+				protdist \
+				protpars \
+				restdist \
+				restml \
+				retree \
+				seqboot \
+				treedist \
+        		drawgram \
+				drawtree 
+							
+DYLIBS  =       libdrawgram.so \
+		        libdrawtree.so
+
+JARS    =       javajars/DrawGram.jar \
+                javajars/DrawTree.jar \
+                javajars/DrawGramJava.unx\
+                javajars/DrawTreeJava.unx
+#
+# general commands
+#
+
+#  The first target it executed if you just type "make".  It tells you how to
+#  use the Makefile.
+#
+help:
+	@echo ""
+	@echo " To use the PHYLIP v3.6 Makefile, type"
+	@echo "     make install       to compile the whole package and install"
+	@echo "                          the executables in $(EXEDIR), and then"
+	@echo "                          remove the object files to save space"
+	@echo "     make all           to compile the whole package but not install it"
+	@echo "                          or remove the object files"
+	@echo "     make put           to move the executables into $(EXEDIR)"
+	@echo "     make clean         to remove all object files and executables from the"
+	@echo "                          current directory"
+	@echo "     make dnaml         to compile and link one program, (in this example,"
+	@echo "                          Dnaml) and leave the executable and object files"
+	@echo "                          in the current directory (where the source code is)."
+	@echo "                          You will have to move the executable into the"
+	@echo "                          executables directory (e.g. \"mv dnaml $(EXEDIR)\")"
+	@echo "                          Note that the program name should be lower case."
+	@echo " "
+
+introduce:
+	@echo "Building PHYLIP version $(VERSION)"
+
+all:        introduce $(PROGS) $(DYLIBS)
+	@echo "Finished compiling."
+	@echo ""
+
+install:        all put clean
+	@echo "Done."
+	@echo ""
+
+put:
+	@echo "Installing PHYLIP v3.6 binaries in $(EXEDIR)"
+	@mkdir -p $(EXEDIR)
+	@cp $(PROGS) $(EXEDIR)
+	#@cp $(DYLIBS) $(EXEDIR)
+	#@cp $(JARS) $(EXEDIR)
+	@echo "Installing font files in $(DATADIR)"
+	@mkdir -p $(DATADIR)
+	@cp font* $(DATADIR)
+	@cd $(DATADIR) && ln -s font1 fontfile
+	@echo "Finished installation."
+	@echo ""
+
+clean:
+	@echo "Removing object files to save space"
+	@rm -f *.o
+	@echo "Finished removing object files.  Now will remove"
+	@echo "executable files from the current directory, but not from the"
+	@echo "executables directory.  (If some are not here, the makefile"
+	@echo "will terminate with an error message but this is not a problem)"
+	@echo ""
+	@echo "Removing executables from this directory"
+	@rm -f $(PROGS)
+	@echo "Finished cleanup."
+	@echo ""
+
+distclean: clean
+	@echo "Removing executables"
+	@rm -rf $(EXEDIR)/* $(DATADIR)/*
+	@echo "Finaly removed all executable files."
+	@echo ""
+
+#
+# compile object files shared between programs
+# (make's implicit rule for %.o will take care of these)
+#
+
+phylip.o:     phylip.h
+seq.o:        phylip.h seq.h
+disc.o:       phylip.h disc.h
+discrete.o:   phylip.h discrete.h
+dollo.o:      phylip.h dollo.h
+wagner.o:     phylip.h wagner.h
+dist.o:       phylip.h dist.h
+cont.o:       phylip.h cont.h
+mlclock.o:    phylip.h mlclock.h
+moves.o:      phylip.h moves.h
+printree.o:   phylip.h printree.h
+
+#
+# compile the individual programs
+#
+
+clique.o:       clique.c disc.h phylip.h
+
+clique:         clique.o disc.o phylip.o
+	$(CC) $(CFLAGS) clique.o disc.o phylip.o $(LIBS) -o clique
+
+cons.o:         cons.c cons.h phylip.h 
+
+consense.o:     consense.c cons.h phylip.h
+
+consense:       consense.o phylip.o cons.o
+	$(CC) $(CFLAGS) consense.o phylip.o cons.o $(LIBS) -o consense
+
+contml.o:       contml.c cont.h phylip.h
+
+contml:       contml.o cont.o phylip.o
+	$(CC) $(CFLAGS) contml.o cont.o phylip.o $(LIBS) -o contml
+
+contrast.o:       contrast.c cont.h phylip.h
+
+contrast:       contrast.o cont.o phylip.o
+	$(CC) $(CFLAGS) contrast.o cont.o phylip.o $(LIBS) -o contrast
+
+dnacomp.o:      dnacomp.c seq.h phylip.h
+
+dnacomp:      dnacomp.o seq.o phylip.o
+	$(CC) $(CFLAGS) dnacomp.o seq.o phylip.o $(LIBS) -o dnacomp
+
+dnadist.o:      dnadist.c seq.h phylip.h
+
+dnadist:      dnadist.o seq.o phylip.o
+	$(CC) $(CFLAGS) dnadist.o seq.o phylip.o $(LIBS) -o dnadist
+
+dnainvar.o:      dnainvar.c seq.h phylip.h
+
+dnainvar:      dnainvar.o seq.o phylip.o
+	$(CC) $(CFLAGS) dnainvar.o seq.o phylip.o $(LIBS) -o dnainvar
+
+dnaml.o:      dnaml.c seq.h phylip.h
+
+dnaml:      dnaml.o seq.o phylip.o
+	$(CC) $(CFLAGS) dnaml.o seq.o phylip.o $(LIBS) -o dnaml
+
+dnamlk.o:      dnamlk.c seq.h phylip.h mlclock.h printree.h
+
+dnamlk:      dnamlk.o seq.o phylip.o mlclock.o printree.o
+	$(CC) $(CFLAGS) dnamlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o dnamlk
+
+dnamove.o:      dnamove.c seq.h moves.h phylip.h
+
+dnamove:      dnamove.o seq.o moves.o phylip.o
+	$(CC) $(CFLAGS) dnamove.o seq.o moves.o phylip.o $(LIBS) -o dnamove
+
+dnapenny.o:      dnapenny.c seq.h phylip.h
+
+dnapenny:      dnapenny.o seq.o phylip.o
+	$(CC) $(CFLAGS) dnapenny.o seq.o phylip.o $(LIBS) -o dnapenny
+
+dnapars.o:      dnapars.c seq.h phylip.h
+
+dnapars:      dnapars.o seq.o phylip.o
+	$(CC) $(CFLAGS) dnapars.o seq.o phylip.o $(LIBS) -o dnapars
+
+dolmove.o:       dolmove.c disc.h moves.h dollo.h phylip.h
+
+dolmove:       dolmove.o disc.o moves.o dollo.o phylip.o
+	$(CC) $(CFLAGS) dolmove.o disc.o moves.o dollo.o phylip.o $(LIBS) -o dolmove
+
+dollop.o:       dollop.c disc.h dollo.h phylip.h
+
+dollop:       dollop.o disc.o dollo.o phylip.o
+	$(CC) $(CFLAGS) dollop.o disc.o dollo.o phylip.o $(LIBS) -o dollop
+
+dolpenny.o:       dolpenny.c disc.h dollo.h phylip.h
+
+dolpenny:       dolpenny.o disc.o dollo.o phylip.o
+	$(CC) $(CFLAGS) dolpenny.o disc.o dollo.o phylip.o $(LIBS) -o dolpenny
+
+draw.o:   draw.c draw.h phylip.h 
+	$(CC) $(DFLAGS) -c draw.c
+
+draw2.o:   draw2.c draw.h phylip.h 
+	$(CC) $(DFLAGS) -c draw2.c
+
+drawgram.o:     drawgram.c draw.h phylip.h
+	$(CC) $(DFLAGS) -c drawgram.c
+
+drawgram:     drawgram.o draw.o draw2.o phylip.o
+	$(CC) $(DFLAGS) draw.o draw2.o drawgram.o phylip.o $(DLIBS) -o drawgram
+	
+# needed by java	
+libdrawgram.so:   drawgram.o draw.o draw2.o phylip.o
+	$(CC) $(CFLAGS) -o libdrawgram.so -shared -fPIC drawgram.c draw.c draw2.c phylip.c $(CLIBS) $(LDFLAGS)
+
+drawtree.o:     drawtree.c draw.h phylip.h
+	$(CC) $(DFLAGS)  -shared -fPIC -c drawtree.c
+
+drawtree:     drawtree.o draw.o draw2.o phylip.o
+	$(CC) $(DFLAGS) draw.o draw2.o drawtree.o phylip.o $(DLIBS) -o drawtree
+
+# needed by java	
+libdrawtree.so:     drawtree.o draw.o draw2.o phylip.o
+	$(CC) $(CFLAGS) -o libdrawtree.so  -shared -fPIC drawtree.c draw.c draw2.c phylip.c $(CLIBS) $(LDFLAGS)
+
+factor.o:       factor.c phylip.h
+
+factor:       factor.o phylip.o
+	$(CC) $(CFLAGS) factor.o phylip.o $(LIBS) -o factor
+
+fitch.o:        fitch.c dist.h phylip.h
+
+fitch:        fitch.o dist.o phylip.o
+	$(CC) $(CFLAGS) fitch.o dist.o phylip.o $(LIBS) -o fitch
+
+gendist.o:      gendist.c phylip.h
+
+gendist:      gendist.o phylip.o
+	$(CC) $(CFLAGS) gendist.o phylip.o $(LIBS) -o gendist
+
+kitsch.o:        kitsch.c dist.h phylip.h
+
+kitsch:        kitsch.o dist.o phylip.o
+	$(CC) $(CFLAGS) kitsch.o dist.o phylip.o $(LIBS) -o kitsch
+
+mix.o:        mix.c disc.h wagner.h phylip.h
+
+mix:        mix.o disc.o wagner.o phylip.o
+	$(CC) $(CFLAGS) mix.o disc.o wagner.o phylip.o $(LIBS) -o mix
+
+move.o:        move.c disc.h moves.h wagner.h phylip.h
+
+move:        move.o disc.o moves.o wagner.o phylip.o
+	$(CC) $(CFLAGS) move.o disc.o moves.o wagner.o phylip.o $(LIBS) -o move
+
+neighbor.o:        neighbor.c dist.h phylip.h
+
+neighbor:        neighbor.o dist.o phylip.o
+	$(CC) $(CFLAGS) neighbor.o dist.o phylip.o $(LIBS) -o neighbor
+
+pars.o:   pars.c discrete.h phylip.h
+
+pars: pars.o discrete.o phylip.o
+	$(CC) $(CFLAGS) pars.o discrete.o phylip.o $(LIBS) -o pars
+
+penny.o:  penny.c disc.h wagner.h phylip.h
+
+penny:  penny.o disc.o wagner.o phylip.o
+	$(CC) $(CFLAGS) penny.o disc.o wagner.o  phylip.o $(LIBS) -o penny
+
+proml.o:      proml.c seq.h phylip.h
+
+proml:      proml.o seq.o phylip.o
+	$(CC) $(CFLAGS) proml.o seq.o phylip.o $(LIBS) -o proml
+
+promlk.o:      promlk.c seq.h phylip.h mlclock.h printree.h
+
+promlk:      promlk.o seq.o phylip.o mlclock.o printree.o
+	$(CC) $(CFLAGS) promlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o promlk
+
+protdist.o:      protdist.c seq.h phylip.h
+
+protdist:      protdist.o seq.o phylip.o
+	$(CC) $(CFLAGS) protdist.o seq.o phylip.o $(LIBS) -o protdist
+
+protpars.o: protpars.c seq.h phylip.h
+
+protpars: protpars.o seq.o phylip.o
+	$(CC) $(CFLAGS) protpars.o seq.o phylip.o $(LIBS) -o protpars
+
+restdist.o: restdist.c seq.h phylip.h
+
+restdist: restdist.o seq.o phylip.o
+	$(CC) $(CFLAGS) restdist.o seq.o phylip.o $(LIBS) -o restdist
+
+restml.o: restml.c seq.h phylip.h
+
+restml: restml.o seq.o phylip.o
+	$(CC) $(CFLAGS) restml.o seq.o phylip.o $(LIBS) -o restml
+
+retree.o:       retree.c moves.h phylip.h
+
+retree:       retree.o moves.o phylip.o
+	$(CC) $(CFLAGS) retree.o moves.o phylip.o $(LIBS) -o retree
+
+seqboot.o:      seqboot.c phylip.h
+
+seqboot:      seqboot.o seq.o phylip.o
+	$(CC) $(CFLAGS) seqboot.o seq.o phylip.o $(LIBS) -o seqboot
+
+treedist.o:     treedist.c cons.h phylip.h
+
+treedist:     treedist.o phylip.o cons.o
+	$(CC) $(CFLAGS) treedist.o cons.o phylip.o $(LIBS) -o treedist
+
+
+# ----------------------------------------------------------------------------
+#  The following section is used to build a PHYLIP distribution. All sources
+#  and other files except the documentation files must be placed in the
+#  current directory.  The HTML documentation files must be in folder "doc"
+#  within this, the Mac icons in folder "mac", and the Windows icons and
+#  resource files must be in folder "icons"
+#
+#  Usage:
+#  	make distdir	- Build the distribution dir phylip-<vers>/
+#  	make dist	- Make a tarred and gzipped phylip-<vers>.tar.gz
+# ----------------------------------------------------------------------------
+
+DIST_COMMON = phylip.html 
+
+DOCS= doc/clique.html doc/consense.html doc/contchar.html doc/contml.html \
+      doc/contrast.html doc/discrete.html doc/distance.html doc/dnacomp.html \
+      doc/dnadist.html doc/dnainvar.html doc/dnaml.html doc/dnamlk.html \
+      doc/dnamove.html doc/dnapars.html doc/dnapenny.html doc/dollop.html \
+      doc/dolmove.html doc/dolpenny.html doc/drawgram.html doc/draw.html \
+      doc/drawtree.html doc/factor.html doc/fitch.html doc/gendist.html \
+      doc/kitsch.html doc/main.html doc/mix.html doc/move.html \
+      doc/neighbor.html doc/pars.html doc/penny.html doc/proml.html \
+      doc/promlk.html doc/protdist.html doc/protpars.html doc/restdist.html \
+      doc/restml.html doc/retree.html doc/seqboot.html doc/sequence.html \
+      doc/treedist.html doc/phylip.gif
+
+SOURCES= COPYRIGHT Makefile Makefile.cyg Makefile.osx Makefile.unx linkmac  \
+     clique.c cons.c consense.c cons.h cont.c \
+     cont.h contml.c contrast.c disc.c disc.h discrete.c discrete.h dist.c \
+	 dist.h dnacomp.c dnadist.c dnainvar.c dnaml.c dnamlk.c dnamove.c \
+	 dnapars.c dnapenny.c dollo.c dollo.h dollop.c dolmove.c dolpenny.c \
+	 draw2.c draw.c drawgram.c draw.h drawtree.c \
+	 factor.c fitch.c gendist.c \
+	 kitsch.c mix.c move.c \
+	 moves.c moves.h neighbor.c pars.c penny.c \
+	 phylip.c phylip.h proml.c promlk.c protdist.c protpars.c restdist.c \
+	 restml.c retree.c seqboot.c seq.c seq.h treedist.c wagner.c wagner.h \
+	 mlclock.c mlclock.h printree.c printree.h
+
+MAC= \
+		Info.plist.in boot.icns clique.icns command.in consense.icns \
+	contml.icns contrast.icns disc.icns dist.icns dna.icns dnacomp.icns \
+	dnadist.icns dnainvar.icns dnaml.icns dnamlk.icns dnamove.icns \
+	dnapars.icns dnapenny.icns dollo.icns dollop.icns dolmove.icns \
+	dolpenny.icns drawgram.icns drawtree.icns factor.icns fitch.icns \
+	gendist.icns kitsch.icns mac.sit mix.icns move.icns neighbor.icns \
+	pars.icns penny.icns proml.icns promlk.icns protdist.icns protein.icns \
+	protpars.icns restdist.icns restml.icns restrict.icns retree.icns \
+	seqboot.icns treedist.icns
+
+ICONS= 		boot.ico clique.ico clique.rc clique.rcb consense.ico \
+		consense.rc consense.rcb contml.ico contml.rc contml.rcb \
+		contrast.ico contrast.rc contrast.rcb disc.ico dist.ico dna.ico \
+		dnacomp.rc dnacomp.rcb dnadist.rc dnadist.rcb dnainvar.rc \
+		dnainvar.rcb dnaml.rc dnaml.rcb dnamlk.rc dnamlk.rcb dnamove.rc \
+		dnamove.rcb dnapars.rc dnapars.rcb dnapenny.rc dnapenny.rcb \
+		dollo.ico dollop.rc dollop.rcb dolmove.rc dolmove.rcb \
+		dolpenny.rc dolpenny.rcb drawgram.ico drawgram.rc drawgram.rcb \
+		drawtree.ico drawtree.rc drawtree.rcb factor.rc factor.rcb \
+		fitch.rc fitch.rcb gendist.ico gendist.rc gendist.rcb kitsch.rc \
+		kitsch.rcb mix.rc mix.rcb move.rc move.rcb neighbor.rc \
+		neighbor.rcb pars.rc pars.rcb penny.rc penny.rcb proml.rc \
+		proml.rcb promlk.rc promlk.rcb protdist.rc protdist.rcb \
+		protein.ico protpars.rc protpars.rcb restdist.rc restdist.rcb \
+		restml.rc restml.rcb restrict.ico retree.ico retree.rc \
+		retree.rcb seqboot.rc seqboot.rcb treedist.ico treedist.rc \
+		treedist.rcb
+
+FONTS= font1 font2 font3 font4 font5 font6
+
+TESTDIR=   clique consense contml contrast dnacomp \
+      dnadist dnainvar dnaml dnamlk dnamove dnapars dnapenny dollop \
+      dolmove dolpenny drawgram drawtree factor fitch gendist \
+      kitsch mix move neighbor pars penny proml promlk \
+      protdist protpars restdist restml retree seqboot  treedist
+      
+JARAJAR=    javajars/DrawGram.jar javajars/DrawTree.jar \
+        javajars/DrawGramJava.bat javajars/DrawTreeJava.bat \
+        javajars/DrawGramJava.exe javajars/DrawTreeJava.exe \
+        javajars/DrawGramJava.unx javajars/DrawTreeJava.unx
+ 
+DISTDIR=$(PACKAGE)-$(VERSION)
+dist_SRCDIR=$(DISTDIR)/src
+dist_DOCDIR=$(DISTDIR)/doc
+dist_EXEDIR=$(DISTDIR)/exe
+dist_JAVADIR=$(DISTDIR)/src/javajars
+MACICONDIR=src/mac
+
+SHELL=bash
+
+# We use this target to create a tarred and gzipped distribution of PHYLIP
+dist: distdir
+	-chmod -R a+r $(DISTDIR)
+	tar chozf $(DISTDIR).tar.gz $(DISTDIR)
+	-rm -rf $(DISTDIR)
+
+# This target creates the distribution directory
+distdir: $(DIST_COMMON) $(DOCS) $(SOURCES)
+	-rm -rf $(DISTDIR)
+	mkdir $(DISTDIR) && \
+	mkdir $(dist_EXEDIR) && \
+	mkdir $(dist_DOCDIR) && \
+	mkdir $(dist_SRCDIR) && \
+	mkdir $(dist_JAVADIR)
+	mkdir $(dist_SRCDIR)/mac
+	mkdir $(dist_SRCDIR)/icons
+	mkdir $(dist_EXEDIR)/testdata
+	for i in $(TESTDIR); do \
+      mkdir $(dist_EXEDIR)/testdata/$$i; \
+      cp TestData/$$i/*.txt $(dist_EXEDIR)/testdata/$$i; \
+    done
+	for i in $(DIST_COMMON) ; do \
+	  cp -r $$i $(DISTDIR) ; \
+	done
+	for i in $(DOCS) ; do \
+	  cp -r $$i $(dist_DOCDIR) ; \
+	done
+	for i in $(SOURCES) ; do \
+	  cp -r $$i $(dist_SRCDIR) ; \
+	done
+	for i in $(MAC) ; do \
+	  cp -r mac/$$i $(dist_SRCDIR)/mac ; \
+	done
+	for i in $(ICONS) ; do \
+	  cp -r icons/$$i $(dist_SRCDIR)/icons ; \
+	done
+	for i in $(FONTS) ; do \
+	  cp -r $$i $(dist_SRCDIR) ; \
+	done
+	for i in $(JARAJAR) ; do \
+	  cp $$i $(dist_JAVADIR) ; \
+	done
+
+# This target untars the dist and checks that it can be compiled and remade
+distcheck: dist
+	-rm -rf $(DISTDIR)
+	tar xzf $(DISTDIR).tar.gz
+	cd $(DISTDIR)/$(SRCDIR) \
+	  && make all
+	-rm -rf $(DISTDIR)
+	@echo "$(DISTDIR).tar.gz is ready for distribution"
+
+# Makefile

=== modified file 'debian/README.debian'
--- debian/README.debian	2008-07-22 15:51:33 +0000
+++ debian/README.debian	2015-04-04 21:58:41 +0000
@@ -21,9 +21,3 @@
 
 http://evolution.genetics.washington.edu/phylip.html
 
-The original packaging was done by:
-  Dr. Guenter Bechly <[e-mail]>, Sat, 7 Apr 2001 16:00:14 +0200
-
-The current Debian Maintainer is:
-  Andreas Tille <[e-mail]>  Tue, 23 Oct 2001 12:35:14 +0200
-  
\ No newline at end of file

=== removed file 'debian/README.source'
--- debian/README.source	2009-09-11 08:00:10 +0000
+++ debian/README.source	1970-01-01 00:00:00 +0000
@@ -1,4 +0,0 @@
-This packages uses the quilt patch system. Please read
-/usr/share/doc/quilt/README.source for more information.
-
- -- Andreas Tille <[e-mail]>  Mon, 31 Aug 2009 14:50:19 +0200

=== added directory 'debian/bash_completion'
=== added file 'debian/bash_completion/phylip'
--- debian/bash_completion/phylip	1970-01-01 00:00:00 +0000
+++ debian/bash_completion/phylip	2015-04-04 21:58:41 +0000
@@ -0,0 +1,17 @@
+_phylip()
+{
+  local cur prev opts
+  COMPREPLY=()
+  cur="${COMP_WORDS[COMP_CWORD]}"
+  prev="${COMP_WORDS[COMP_CWORD-1]}"
+
+  opts=$(ls /usr/lib/phylip/bin)
+
+  case $prev in
+      phylip)
+          COMPREPLY=( $(compgen -f -W "${opts}" -- "$cur") )
+          ;;
+  esac
+  return 0
+}
+complete -F _phylip -o default phylip

=== added file 'debian/bin/drawgram'
--- debian/bin/drawgram	1970-01-01 00:00:00 +0000
+++ debian/bin/drawgram	2015-04-04 21:58:41 +0000
@@ -0,0 +1,3 @@
+#!/bin/sh
+export PATH=/usr/lib/phylip/bin:$PATH
+java -cp DrawTree.jar  drawgram.DrawgramUserInterface

=== added file 'debian/bin/drawtree'
--- debian/bin/drawtree	1970-01-01 00:00:00 +0000
+++ debian/bin/drawtree	2015-04-04 21:58:41 +0000
@@ -0,0 +1,3 @@
+#!/bin/sh
+export PATH=/usr/lib/phylip/bin:$PATH
+java -cp DrawTree.jar drawtree.DrawtreeUserInterface

=== added file 'debian/build.xml'
--- debian/build.xml	1970-01-01 00:00:00 +0000
+++ debian/build.xml	2015-04-04 21:58:41 +0000
@@ -0,0 +1,57 @@
+<?xml  version="1.0" ?>
+<project name="drawtree" default="jar" basedir=".">
+    <!-- Directory structure -->
+    <property name="build.dir" location="build"/>
+    <property name="dist.dir" location="dist"/>
+    <property name="src.dir" location="src/javasrc"/>
+    <property name="lib.dir" location="/usr/share/java"/>
+    <property name="class.dir" location="${build.dir}/classes"/>
+    
+    <property name="project.name" value="drawphylip"/>
+    <property name="debug" value="true"/>
+    <property name="optimized" value="true"/>
+    <property name="project.version" value="3.696"/>
+    <property environment="env"/>
+    <property name="project.jarfile.name" value="DrawTree.jar"/>   
+    
+    <property name="class.path" value="jna.jar"/>
+                                
+    <path id="compile.classpath">
+            <fileset dir="${lib.dir}">
+            </fileset>
+            <fileset dir="${dist.dir}">
+                <include name="*.jar"/>
+            </fileset>
+    </path>
+    
+    
+    <target name="clean">
+        <echo level="info">Cleaning build directories</echo>
+        <delete verbose="true" includeEmptyDirs="true">
+            <fileset dir="${build.dir}" includes="**"/>
+            <fileset dir="${dist.dir}" includes="${project.name}*.jar"/>
+        </delete>
+    </target>
+    
+    <target name="compile">
+        <mkdir dir="${class.dir}"/>
+        <mkdir dir="${dist.dir}"/>
+        <javac srcdir="${src.dir}" destdir="${class.dir}" classpathref="compile.classpath" debug="${debug}" optimize="${optimized}" nowarn="true" source="1.6" target="1.6">
+        </javac>
+    </target>
+
+    <target name="jar" depends="compile">
+        <jar destfile="${dist.dir}/${project.jarfile.name}" basedir="${class.dir}" >
+         <manifest>
+             <attribute name="Built-By" value="Debian-Med team"/>
+             <attribute name="Main-Class" value="drawtree"/>
+             <attribute name="Class-Path" value="${class.path}"/>
+             <attribute name="Specification-Title" value="drawtree"/>
+             <attribute name="Specification-Version" value="${project.version}"/>
+          </manifest>
+        </jar>
+    </target>
+    
+</project>
+
+

=== modified file 'debian/changelog'
--- debian/changelog	2013-08-07 22:17:03 +0000
+++ debian/changelog	2015-04-04 21:58:41 +0000
@@ -1,3 +1,21 @@
+phylip (1:3.696+dfsg-1ubuntu0.1) trusty-proposed; urgency=medium
+
+  * Use optimization flags by default when compiling 
+
+ -- Atanas <atanas@marash>  Sat, 04 Apr 2015 23:43:16 +0200
+
+phylip (1:3.696+dfsg-1) unstable; urgency=medium
+
+  * New upstream version now with free license
+  * cme fix dpkg-control
+  * removed redundant README.source
+  * d/copyright:
+     - DEP5 now with BSD-2-Clause license
+     - exclude some binaries without source which are not needed
+  * Add bash_completion
+
+ -- Andreas Tille <[e-mail]>  Wed, 17 Sep 2014 19:35:06 +0200
+
 phylip (1:3.695-1) unstable; urgency=low
 
   * New upstream version

=== modified file 'debian/control'
--- debian/control	2013-08-07 22:17:03 +0000
+++ debian/control	2015-04-04 21:58:41 +0000
@@ -2,17 +2,20 @@
 Maintainer: Debian Med Packaging Team <[e-mail]>
 Uploaders: Andreas Tille <[e-mail]>,
            Manuel Prinz <[e-mail]>
-Section: non-free/science
+Section: science
 Priority: optional
 Build-Depends: debhelper (>= 9),
                libx11-dev,
                libxt-dev,
-               libxaw7-dev
-Standards-Version: 3.9.4
+               libxaw7-dev,
+               ant,
+               default-jdk,
+               libjna-java,
+               javahelper
+Standards-Version: 3.9.5
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/phylip/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/phylip/trunk/
 Homepage: http://evolution.genetics.washington.edu/phylip.html
-XS-Autobuild: yes
 
 Package: phylip
 Architecture: any
@@ -30,7 +33,7 @@
 
 Package: phylip-doc
 Architecture: all
-Section: non-free/doc
+Section: doc
 Depends: ${misc:Depends}
 Suggests: phylip
 Description: package of programs for inferring phylogenies (documentation)
@@ -43,4 +46,3 @@
  characters. 
  .
  This package contains the HTML documentation
-

=== modified file 'debian/copyright'
--- debian/copyright	2008-02-12 18:29:32 +0000
+++ debian/copyright	2015-04-04 21:58:41 +0000
@@ -1,35 +1,49 @@
-This package was debianized by Andreas Tille <[e-mail]> on
-Tue, 30 Oct 2001 07:09:09 +0100
-
-It was downloaded from 
-   ftp://evolution.genetics.washington.edu/pub/phylip
-
-The home page is:
-   http://evolution.genetics.washington.edu/phylip.html
-Further Information on:
-   http://evolution.genetics.washington.edu/phylip/software.html
-
-Upstream author:
-
-Joe Felsenstein <[e-mail]>
-http://evolution.genetics.washington.edu/phylip/felsenstein.html
-
-
-Copyright Notice for PHYLIP
-   http://evolution.genetics.washington.edu/phylip/doc/main.html#copyright
-
-The following copyright notice is intended to cover all source code, all
-documentation, and all executable programs of the PHYLIP package.
-
-© Copyright 1980-2004. University of Washington and Joseph Felsenstein. All
-rights reserved. Permission is granted to reproduce, perform, and modify these
-programs and documentation files. Permission is granted to distribute or
-provide access to these programs provided that this copyright notice is not
-removed, the programs are not integrated with or called by any product or
-service that generates revenue, and that your distribution of these
-documentation files and programs are free. Any modified versions of these
-materials that are distributed or accessible shall indicate that they are based
-on these program. Institutions of higher education are granted permission to
-distribute this material to their students and staff for a fee to recover
-distribution costs. Permission requests for any other distribution of this
-program should be directed to  license @ u.washington.edu . 
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: PHYLIP
+Upstream-Contact: Joe Felsenstein <[e-mail]>
+Source: http://evolution.gs.washington.edu/phylip/download/
+Files-Excluded: *.exe
+                *.jar
+                *.so
+                src/buildDmg.sh
+                src/mac
+                src/javajars
+                src/icons
+                src/Makefile.osx
+                src/Makefile.cyg
+                src/javasrc/util/CVS
+
+Files: *
+Copyright: 1980-2014 Joe Felsenstein <[e-mail]>,
+                     Jerry Shurman, Hisashi Horino, Akiko Fuseki,
+                     Sean Lamont, and Andrew Keeffe
+License: BSD-2-clause
+
+Files: debian/*
+Copyright: 1998-1999 Stephane Bortzmeyer <[e-mail]>
+           2001 Dr. Guenter Bechly <[e-mail]>
+           2001-2014 Andreas Tille <[e-mail]>
+License: BSD-2-clause
+
+License: BSD-2-clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ .
+   1. Redistributions of source code must retain the above copyright notice,
+      this list of conditions and the following disclaimer.
+ .
+   2. Redistributions in binary form must reproduce the above copyright notice,
+      this list of conditions and the following disclaimer in the documentation
+      and/or other materials provided with the distribution.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+ LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ POSSIBILITY OF SUCH DAMAGE.

=== modified file 'debian/patches/01_src_phylip_h'
--- debian/patches/01_src_phylip_h	2013-08-07 22:17:03 +0000
+++ debian/patches/01_src_phylip_h	2015-04-04 21:58:41 +0000
@@ -2,9 +2,9 @@
 Forwarded: No
 Description: Debian keeps the font files in a different location than normal installer
 License: see debian/copyright 
---- a/src/phylip.h
-+++ b/src/phylip.h
-@@ -72,7 +72,7 @@ void phyFillScreenColor(void);
+--- phylip-3.696.orig/src/phylip.h
++++ phylip-3.696/src/phylip.h
+@@ -96,7 +96,7 @@
  #define EBCDIC false
  #define INFILE "infile"
  #define OUTFILE "outfile"

=== added file 'debian/patches/do_not_install_jar_files.patch'
--- debian/patches/do_not_install_jar_files.patch	1970-01-01 00:00:00 +0000
+++ debian/patches/do_not_install_jar_files.patch	2015-04-04 21:58:41 +0000
@@ -0,0 +1,20 @@
+Author: Andreas Tille <[e-mail]>
+Last-Update: Wed, 17 Sep 2014 19:35:06 +0200
+Description: The binary JAR files without source are stripped from the
+ source tarball so do not try to install these files
+
+--- a/src/Makefile.unx
++++ b/src/Makefile.unx
+@@ -225,10 +225,8 @@ put:
+ 	@echo "Installing PHYLIP v3.6 binaries in $(EXEDIR)"
+ 	@mkdir -p $(EXEDIR)
+ 	@cp $(PROGS) $(EXEDIR)
+-	@echo "Installing dynamic libraries in $(EXEDIR)"
+-	@cp $(DYLIBS) $(EXEDIR)
+-	@echo "Installing jar files in $(EXEDIR)"
+-	@cp $(JARS) $(EXEDIR)
++	#@cp $(DYLIBS) $(EXEDIR)
++	#@cp $(JARS) $(EXEDIR)
+ 	@echo "Installing font files in $(DATADIR)"
+ 	@mkdir -p $(DATADIR)
+ 	@cp font* $(DATADIR)

=== modified file 'debian/patches/hardening.patch'
--- debian/patches/hardening.patch	2013-08-07 22:17:03 +0000
+++ debian/patches/hardening.patch	2015-04-04 21:58:41 +0000
@@ -2,9 +2,9 @@
 LastChanged: Wed, 07 Aug 2013 22:17:03 +0200
 Description: Let hardening flags sneek in
 
---- a/src/Makefile.unx
-+++ b/src/Makefile.unx
-@@ -126,7 +126,7 @@ DFLAGS = $(CFLAGS)
+--- phylip-3.696.orig/src/Makefile.unx
++++ phylip-3.696/src/Makefile.unx
+@@ -126,7 +126,7 @@
  #
  # Most of the programs need only the math libraries, specified like this;
  #
@@ -13,7 +13,7 @@
  #
  # The drawing programs may also need access to the graphics libraries. This is
  # specified with the DLIBS variable.
-@@ -380,7 +380,7 @@ drawgram:     drawgram.o draw.o draw2.o
+@@ -367,7 +367,7 @@
  	
  # needed by java	
  libdrawgram.so:   drawgram.o draw.o draw2.o phylip.o
@@ -22,7 +22,7 @@
  
  drawtree.o:     drawtree.c draw.h phylip.h
  	$(CC) $(DFLAGS)  -shared -fPIC -c drawtree.c
-@@ -390,7 +390,7 @@ drawtree:     drawtree.o draw.o draw2.o
+@@ -377,7 +377,7 @@
  
  # needed by java	
  libdrawtree.so:     drawtree.o draw.o draw2.o phylip.o

=== modified file 'debian/patches/install_fonts_data.patch'
--- debian/patches/install_fonts_data.patch	2013-08-07 22:17:03 +0000
+++ debian/patches/install_fonts_data.patch	2015-04-04 21:58:41 +0000
@@ -3,9 +3,9 @@
 Description: Debian keeps the font files in a different location than normal installer;
  distclean target makes sure everything will be cleaned up
 
---- a/src/Makefile.unx
-+++ b/src/Makefile.unx
-@@ -51,6 +51,7 @@ VERSION=3.695
+--- phylip-3.696.orig/src/Makefile.unx
++++ phylip-3.696/src/Makefile.unx
+@@ -51,6 +51,7 @@
  #
  # the following specifies the directory where the executables will be placed
  EXEDIR  = ../exe
@@ -13,7 +13,7 @@
  #
  # ----------------------------------------------------------------------------
  #
-@@ -235,8 +236,10 @@ put:
+@@ -228,8 +229,10 @@
  	@cp $(DYLIBS) $(EXEDIR)
  	@echo "Installing jar files in $(EXEDIR)"
  	@cp $(JARS) $(EXEDIR)
@@ -23,16 +23,16 @@
 +	@mkdir -p $(DATADIR)
 +	@cp font* $(DATADIR)
 +	@cd $(DATADIR) && ln -s font1 fontfile
- 	@echo "Copying testdata files to $(EXEDIR)/testdata/..."
- 	mkdir $(EXEDIR)/testdata
- 	for i in $(TESTDIR); do \
-@@ -259,6 +262,12 @@ clean:
+ 	@echo "Finished installation."
+ 	@echo ""
+ 
+@@ -246,6 +249,12 @@
  	@echo "Finished cleanup."
  	@echo ""
  
 +distclean: clean
 +	@echo "Removing executables"
-+	@rm -rf $(EXEDIR) $(DATADIR)
++	@rm -rf $(EXEDIR)/* $(DATADIR)/*
 +	@echo "Finaly removed all executable files."
 +	@echo ""
 +

=== modified file 'debian/patches/series'
--- debian/patches/series	2013-08-07 22:17:03 +0000
+++ debian/patches/series	2015-04-04 21:58:41 +0000
@@ -1,3 +1,5 @@
 install_fonts_data.patch
 hardening.patch
 01_src_phylip_h
+do_not_install_jar_files.patch
+soname.patch

=== added file 'debian/patches/soname.patch'
--- debian/patches/soname.patch	1970-01-01 00:00:00 +0000
+++ debian/patches/soname.patch	2015-04-04 21:58:41 +0000
@@ -0,0 +1,24 @@
+Author: Andreas Tille <[e-mail]>
+Last-Update: Wed, 17 Sep 2014 19:35:06 +0200
+Description: Add soname to shared libraries
+
+--- a/src/Makefile.unx
++++ b/src/Makefile.unx
+@@ -365,7 +365,7 @@ drawgram:     drawgram.o draw.o draw2.o
+ 	
+ # needed by java	
+ libdrawgram.so:   drawgram.o draw.o draw2.o phylip.o
+-	$(CC) $(CFLAGS) -o libdrawgram.so -shared -fPIC drawgram.c draw.c draw2.c phylip.c $(CLIBS) $(LDFLAGS)
++	$(CC) $(CFLAGS) -o libdrawgram.so -Wl,-soname,libdrawgram.so -shared -fPIC drawgram.c draw.c draw2.c phylip.c $(DLIBS)
+ 
+ drawtree.o:     drawtree.c draw.h phylip.h
+ 	$(CC) $(DFLAGS)  -shared -fPIC -c drawtree.c
+@@ -375,7 +375,7 @@ drawtree:     drawtree.o draw.o draw2.o
+ 
+ # needed by java	
+ libdrawtree.so:     drawtree.o draw.o draw2.o phylip.o
+-	$(CC) $(CFLAGS) -o libdrawtree.so  -shared -fPIC drawtree.c draw.c draw2.c phylip.c $(CLIBS) $(LDFLAGS)
++	$(CC) $(CFLAGS) -o libdrawtree.so -Wl,-soname,libdrawtree.so -shared -fPIC drawtree.c draw.c draw2.c phylip.c $(DLIBS)
+ 
+ factor.o:       factor.c phylip.h
+ 

=== modified file 'debian/phylip-doc.install'
--- debian/phylip-doc.install	2006-09-01 23:30:58 +0000
+++ debian/phylip-doc.install	2015-04-04 21:58:41 +0000
@@ -1,2 +1,2 @@
-doc      usr/share/doc/phylip/html
-phylip.* usr/share/doc/phylip/html
+doc		usr/share/doc/phylip/html
+phylip.html	usr/share/doc/phylip/html

=== modified file 'debian/phylip.examples'
--- debian/phylip.examples	2013-08-07 22:17:03 +0000
+++ debian/phylip.examples	2015-04-04 21:58:41 +0000
@@ -1,2 +1,2 @@
 debian/examples/*
-src/testdata
\ No newline at end of file
+# src/testdata
\ No newline at end of file

=== modified file 'debian/phylip.install'
--- debian/phylip.install	2013-08-07 22:17:03 +0000
+++ debian/phylip.install	2015-04-04 21:58:41 +0000
@@ -1,4 +1,5 @@
-exe/[a-su-z]*		usr/lib/phylip/bin
-exe/t[a-df-z]*		usr/lib/phylip/bin
-fonts/*			usr/share/phylip
-debian/bin/phylip	usr/bin
+exe/*				usr/lib/phylip/bin
+src/lib*.so*			usr/lib
+fonts/*				usr/share/phylip
+debian/bin/*			usr/bin
+debian/bash_completion/*	etc/bash_completion.d

=== added file 'debian/phylip.jlibs'
--- debian/phylip.jlibs	1970-01-01 00:00:00 +0000
+++ debian/phylip.jlibs	2015-04-04 21:58:41 +0000
@@ -0,0 +1,1 @@
+dist/*.jar

=== modified file 'debian/phylip.lintian-overrides'
--- debian/phylip.lintian-overrides	2013-08-07 22:17:03 +0000
+++ debian/phylip.lintian-overrides	2015-04-04 21:58:41 +0000
@@ -1,54 +1,6 @@
 # Seems to be false positives - options are properly set
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/clique
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/consense
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/contml
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/contrast
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dnacomp
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dnadist
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dnainvar
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dnaml
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dnamlk
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dnamove
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dnapars
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dnapenny
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dollop
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dolmove
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dolpenny
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/drawgram
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/drawtree
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/factor
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/fitch
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/gendist
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/kitsch
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/libdrawgram.so
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/libdrawtree.so
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/mix
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/move
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/neighbor
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/pars
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/penny
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/proml
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/promlk
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/protdist
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/protpars
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/restdist
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/restml
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/retree
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/seqboot
-phylip: hardening-no-fortify-functions usr/lib/phylip/bin/treedist
-# No idea why upstream is providing duplicated files - they are small in any case
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/dollop/dollopinfile.txt usr/share/doc/phylip/examples/testdata/mix/mixinfile.txt usr/share/doc/phylip/examples/testdata/pars/parsinfile.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/fitch/fitchinfile.txt usr/share/doc/phylip/examples/testdata/kitsch/kitschinfile.txt usr/share/doc/phylip/examples/testdata/neighbor/neighborinfile.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/dnacomp/dnacompinfile.txt usr/share/doc/phylip/examples/testdata/dnapars/dnaparsinfile.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/drawgram/mammal.txt usr/share/doc/phylip/examples/testdata/drawtree/mammal.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/drawgram/14tip.txt usr/share/doc/phylip/examples/testdata/drawtree/14tip.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/dnaml/dnamlcats.txt usr/share/doc/phylip/examples/testdata/dnamlk/dnamlkcats.txt usr/share/doc/phylip/examples/testdata/proml/promlcats.txt usr/share/doc/phylip/examples/testdata/promlk/promlkcats.txt usr/share/doc/phylip/examples/testdata/protdist/protdistcats.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/drawgram/ape2.txt usr/share/doc/phylip/examples/testdata/drawtree/ape2.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/dnaml/dnamlweights.txt usr/share/doc/phylip/examples/testdata/dnamlk/dnamlkweights.txt usr/share/doc/phylip/examples/testdata/proml/promlweights.txt usr/share/doc/phylip/examples/testdata/promlk/promlkweights.txt usr/share/doc/phylip/examples/testdata/protdist/protdistweights.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/contml/contmlinfile.txt usr/share/doc/phylip/examples/testdata/gendist/gendistinfile.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/dnaml/dnamlinfile.txt usr/share/doc/phylip/examples/testdata/dnamlk/dnamlkinfile.txt usr/share/doc/phylip/examples/testdata/proml/promlinfile.txt usr/share/doc/phylip/examples/testdata/promlk/promlkinfile.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/restdist/restdistoutfile.txt usr/share/doc/phylip/examples/testdata/restml/restmloutfile.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/clique/cliqueinfile.txt usr/share/doc/phylip/examples/testdata/dolmove/dolmoveinfile.txt usr/share/doc/phylip/examples/testdata/move/moveinfile.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/drawgram/cats.txt usr/share/doc/phylip/examples/testdata/drawtree/cats.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/drawgram/ape1.txt usr/share/doc/phylip/examples/testdata/drawtree/ape1.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/restdist/restdistinfile.txt usr/share/doc/phylip/examples/testdata/restml/restmlinfile.txt
+phylip: hardening-no-fortify-functions usr/lib/phylip/bin/*
+phylip: hardening-no-fortify-functions usr/lib/libdraw*.so
+phylip: package-name-doesnt-match-sonames libdrawgram libdrawtree
+phylip: shlib-without-versioned-soname usr/lib/libdraw*.so libdraw*.so
+phylip: no-symbols-control-file usr/lib/libdraw*.so

=== added file 'debian/phylip.postinst'
--- debian/phylip.postinst	1970-01-01 00:00:00 +0000
+++ debian/phylip.postinst	2015-04-04 21:58:41 +0000
@@ -0,0 +1,13 @@
+#!/bin/sh
+
+set -e
+
+case "$1" in
+	configure)
+		ldconfig
+	;;
+	*)
+	;;
+esac
+
+#DEBHELPER#

=== added file 'debian/phylip.postrm'
--- debian/phylip.postrm	1970-01-01 00:00:00 +0000
+++ debian/phylip.postrm	2015-04-04 21:58:41 +0000
@@ -0,0 +1,13 @@
+#!/bin/sh
+
+set -e
+
+case "$1" in
+	remove)
+		ldconfig
+	;;
+	*)
+	;;
+esac
+
+#DEBHELPER#

=== modified file 'debian/rules'
--- debian/rules	2013-08-07 22:17:03 +0000
+++ debian/rules	2015-04-04 21:58:41 +0000
@@ -2,14 +2,24 @@
 # debian/rules for phylip using dh
 # Andreas Tille <[e-mail]>, GPL
 
+DEBPKGNAME		:= $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+DEB_HOST_MULTIARCH	?= $(shell dpkg-architecture -qDEB_HOST_MULTIARCH)
+LIBDIR			:= $(CURDIR)/debian/$(DEBPKGNAME)/usr/lib/ # $(DEB_HOST_MULTIARCH)
+
+export JAVA_HOME=/usr/lib/jvm/default-java
+
 %:
-	dh $@
+	dh $@ --with javahelper
 
 override_dh_auto_build:
 	dh_auto_build --sourcedirectory=src --buildsystem=makefile -- -f Makefile.unx all
+	cp debian/build.xml build.xml
+	ant
 
 override_dh_auto_install:
 	dh_auto_install --sourcedirectory=src --buildsystem=makefile -- -f Makefile.unx install DATADIR=../fonts
+#	mkdir -p $(LIBDIR)
+#	cp -a src/lib*.so* $(LIBDIR)
 
 override_dh_installexamples:
 	dh_installexamples
@@ -17,4 +27,11 @@
 
 override_dh_auto_clean:
 	dh_auto_clean --sourcedirectory=src --buildsystem=makefile -- -f Makefile.unx clean
-	rm -fr exe/* fonts/ src/*.so
+	rm -fr exe/* fonts/ src/*.so*
+	if [ -e build.xml ] ; then \
+	    ant clean ; \
+	    rm -rf dist build.xml ; \
+	fi
+
+get-orig-source:
+	uscan --verbose --force-download --repack --compress xz

=== removed file 'debian/source/lintian-overrides'
--- debian/source/lintian-overrides	2013-08-07 22:17:03 +0000
+++ debian/source/lintian-overrides	1970-01-01 00:00:00 +0000
@@ -1,3 +0,0 @@
-# The package is non-free anyway - so why bothering touching the source
-phylip: source-contains-prebuilt-windows-binary src/javajars/DrawGramJava.exe
-phylip: source-contains-prebuilt-windows-binary src/javajars/DrawTreeJava.exe

=== modified file 'debian/watch'
--- debian/watch	2009-09-11 08:00:10 +0000
+++ debian/watch	2015-04-04 21:58:41 +0000
@@ -1,3 +1,3 @@
 version=3
-
-http://evolution.gs.washington.edu/phylip/download/phylip-(.*)\.tar\.gz
+opts=uversionmangle=s/$/+dfsg/ \
+  http://evolution.gs.washington.edu/phylip/download/phylip-(.*)\.tar\.gz

=== modified file 'doc/clique.html'
--- doc/clique.html	2009-09-11 08:00:10 +0000
+++ doc/clique.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,15 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Clique -- Compatibility Program</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2008 by the University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 This program uses the compatibility method for unrooted two-state
 characters to obtain the largest cliques of characters and the trees

=== modified file 'doc/consense.html'
--- doc/consense.html	2009-09-11 08:00:10 +0000
+++ doc/consense.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,15 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Consense -- Consensus tree program</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2008 by The University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 Consense reads a file of computer-readable trees and prints
 out (and may also write out onto a file) a consensus tree.  At the moment

=== modified file 'doc/contchar.html'
--- doc/contchar.html	2009-09-11 08:00:10 +0000
+++ doc/contchar.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,15 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Gene Frequencies and Continuous Character Data Programs</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2008 by the University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 The programs in this group
 use gene frequencies and quantitative character values.  One (Contml)

=== modified file 'doc/contml.html'
--- doc/contml.html	2009-09-11 08:00:10 +0000
+++ doc/contml.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,15 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Contml - Gene Frequencies and Continuous Characters Maximum Likelihood method</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2008 by the University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 This program estimates phylogenies by the restricted maximum likelihood method
 based on the Brownian motion model.  It is based on the model of Edwards and

=== modified file 'doc/contrast.html'
--- doc/contrast.html	2009-09-11 08:00:10 +0000
+++ doc/contrast.html	2015-04-04 21:58:41 +0000
@@ -10,7 +10,7 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
@@ -20,10 +20,8 @@
 <PRE>
 </PRE>
 <P>
-&#169; Copyright 1991-2008 by the University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 This program implements the contrasts calculation described in my 1985
 paper on the comparative method (Felsenstein, 1985d).  It reads in a

=== modified file 'doc/discrete.html'
--- doc/discrete.html	2009-09-11 08:00:10 +0000
+++ doc/discrete.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,15 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>DOCUMENTATION FOR (0,1) DISCRETE CHARACTER PROGRAMS</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2008 by the University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 These programs are intended for the use of morphological
 systematists who are dealing with discrete characters,

=== modified file 'doc/distance.html'
--- doc/distance.html	2009-09-11 08:00:10 +0000
+++ doc/distance.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,15 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Distance matrix programs</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2008 by the University of Washington.   Written by Joseph
-Felsenstein.  Permission is granted to copy
-this document provided that no fee is charged for it and  that  this  copyright
-notice is not removed.
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 The programs Fitch, Kitsch, and Neighbor are for dealing with  data  which
 comes  in the form of a matrix of pairwise distances between all pairs of taxa,

=== modified file 'doc/dnacomp.html'
--- doc/dnacomp.html	2009-09-11 08:00:10 +0000
+++ doc/dnacomp.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,15 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Dnacomp -- DNA Compatibility Program</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2008 by the University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 </EM>
 This program implements the compatibility method for DNA sequence

=== modified file 'doc/dnadist.html'
--- doc/dnadist.html	2009-09-11 08:00:10 +0000
+++ doc/dnadist.html	2015-04-04 21:58:41 +0000
@@ -10,7 +10,7 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>

=== modified file 'doc/dnainvar.html'
--- doc/dnainvar.html	2009-09-11 08:00:10 +0000
+++ doc/dnainvar.html	2015-04-04 21:58:41 +0000
@@ -10,7 +10,7 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
@@ -18,10 +18,8 @@
 phylogenetic invariants from nucleotide sequences</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2008 by the University of Washington.
-Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 This program reads in nucleotide sequences for four species and computes
 the phylogenetic invariants discovered by James Cavender (Cavender and

=== modified file 'doc/dnaml.html'
--- doc/dnaml.html	2009-09-11 08:00:10 +0000
+++ doc/dnaml.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,15 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Dnaml -- DNA Maximum Likelihood program</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2008 by the University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 This program implements the maximum likelihood method for DNA
 sequences.  The

=== modified file 'doc/dnamlk.html'
--- doc/dnamlk.html	2009-09-11 08:00:10 +0000
+++ doc/dnamlk.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,15 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Dnamlk -- DNA Maximum Likelihood program<BR>with molecular clock</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2008 by the University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 This program implements the maximum likelihood method for DNA
 sequences under the constraint that the trees estimated must be

=== modified file 'doc/dnamove.html'
--- doc/dnamove.html	2009-09-11 08:00:10 +0000
+++ doc/dnamove.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,15 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Dnamove - Interactive DNA parsimony</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2008 by the University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 Dnamove is an interactive DNA parsimony program, inspired by Wayne Maddison and
 David and Wayne Maddison's marvellous program MacClade, which is written for

=== modified file 'doc/dnapars.html'
--- doc/dnapars.html	2009-09-11 08:00:10 +0000
+++ doc/dnapars.html	2015-04-04 21:58:41 +0000
@@ -11,17 +11,15 @@
 <BODY BGCOLOR="#ccffff">
 <P>
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Dnapars -- DNA Parsimony Program</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2008 by The University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 This program carries out unrooted parsimony (analogous to Wagner
 trees) (Eck and Dayhoff, 1966; Kluge and Farris, 1969) on DNA

=== modified file 'doc/dnapenny.html'
--- doc/dnapenny.html	2009-09-11 08:00:10 +0000
+++ doc/dnapenny.html	2015-04-04 21:58:41 +0000
@@ -10,7 +10,7 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
@@ -19,10 +19,8 @@
 for nucleic acid sequence parsimony criteria</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2008 by The University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 Dnapenny is a program that will find all of the most parsimonious trees
 implied by your data when the nucleic acid sequence parsimony criterion is

=== modified file 'doc/dollop.html'
--- doc/dollop.html	2009-09-11 08:00:10 +0000
+++ doc/dollop.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,15 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P> 
 <DIV ALIGN=CENTER>
 <H1>Dollop  -- Dollo and Polymorphism Parsimony Program</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2008 by the University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 This program carries out the Dollo and polymorphism parsimony methods.  The
 Dollo parsimony method was

=== modified file 'doc/dolmove.html'
--- doc/dolmove.html	2009-09-11 08:00:10 +0000
+++ doc/dolmove.html	2015-04-04 21:58:41 +0000
@@ -10,7 +10,7 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
@@ -18,10 +18,8 @@
 </DIV>
 </PRE>
 <P>
-&#169; Copyright 1986-2008 by the University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 Dolmove is an interactive parsimony program which uses the Dollo and 
 Polymorphism parsimony criteria.  It was inspired by Wayne Maddison and

=== modified file 'doc/dolpenny.html'
--- doc/dolpenny.html	2009-09-11 08:00:10 +0000
+++ doc/dolpenny.html	2015-04-04 21:58:41 +0000
@@ -10,7 +10,7 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
@@ -18,10 +18,8 @@
 for Dollo, polymorphism parsimony criteria</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2008 by the University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 Dolpenny is a program that will find all of the most parsimonious trees
 implied by your data when the Dollo or polymorphism parsimony criteria are

=== modified file 'doc/draw.html'
--- doc/draw.html	2013-08-07 22:17:03 +0000
+++ doc/draw.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,16 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.695
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Drawtree and Drawgram</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2013 by The University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+Written by Joseph Felsenstein and James McGill.<br>
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 Drawtree and Drawgram are interactive tree-plotting programs that take a
 tree description in a file and read it, and then let you interactively make

=== modified file 'doc/drawgram.html'
--- doc/drawgram.html	2013-08-07 22:17:03 +0000
+++ doc/drawgram.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,16 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.695
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Drawgram</H1>
 </DIV>
 <P>
-&#169; Copyright 1990-2013 by The University of
-Washington.  Written by Joseph Felsenstein and Jim McGill.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+Written by Joseph Felsenstein and James McGill.<br>
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 </P>
 <P>
 Drawgram interactively plots a cladogram- or phenogram-like rooted tree

=== modified file 'doc/drawtree.html'
--- doc/drawtree.html	2013-08-07 22:17:03 +0000
+++ doc/drawtree.html	2015-04-04 21:58:41 +0000
@@ -18,10 +18,9 @@
 </DIV>
 </p>
 <P>
-&#169; Copyright 1990-2013 by The University of
-Washington.  Written by Joseph Felsenstein and Jim McGill.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+Written by Joseph Felsenstein and James McGill.<br>
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 </P>
 <P>
 Drawtree interactively plots an unrooted tree diagram, with many options

=== modified file 'doc/factor.html'
--- doc/factor.html	2009-09-11 08:00:10 +0000
+++ doc/factor.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,15 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Factor - Program to factor multistate characters.</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2008 by The University of Washington. Written by
-Christopher Meacham and Joseph Felsenstein.  Permission is granted
-to copy this document provided that no fee is charged for it and that this
-copyright notice is not removed.
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 This program factors a data set that contains multistate
 characters, creating a data set consisting entirely of binary (0,1)

=== modified file 'doc/fitch.html'
--- doc/fitch.html	2009-09-11 08:00:10 +0000
+++ doc/fitch.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,15 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Fitch -- Fitch-Margoliash and Least-Squares Distance Methods</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2008 by the University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 This program carries out Fitch-Margoliash, Least Squares,
 and a number of similar methods as described in the documentation

=== modified file 'doc/gendist.html'
--- doc/gendist.html	2009-09-11 08:00:10 +0000
+++ doc/gendist.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,15 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Gendist - Compute genetic distances from gene frequencies</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2008 by the University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 This program computes any one of three measures of genetic distance from a set
 of gene frequencies in different populations (or species).  The three are

=== modified file 'doc/kitsch.html'
--- doc/kitsch.html	2009-09-11 08:00:10 +0000
+++ doc/kitsch.html	2015-04-04 21:58:41 +0000
@@ -10,7 +10,7 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
@@ -18,10 +18,8 @@
 with Evolutionary Clock</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2008 by the University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 This program carries out the Fitch-Margoliash and Least Squares methods,
 plus a variety of others of the same family, with the assumption that all
@@ -38,7 +36,7 @@
 <TABLE><TR><TD BGCOLOR=white>
 <PRE>
 
-Fitch-Margoliash method with contemporary tips, version 3.69
+Fitch-Margoliash method with contemporary tips, version 3.696
 
 Settings for this run:
   D      Method (F-M, Minimum Evolution)?  Fitch-Margoliash

=== modified file 'doc/main.html'
--- doc/main.html	2013-08-07 22:17:03 +0000
+++ doc/main.html	2015-04-04 21:58:41 +0000
@@ -16,9 +16,9 @@
 <P>
 <IMG SRC="phylip.gif" ALT="PHYLIP Logo">
 <P>
-<H3>Version 3.695</H3>
+<H3>Version 3.696</H3>
 <P>
-<H3>April, 2013</H3>
+<H3>September, 2014</H3>
 <P>
 <H2>by Joseph Felsenstein</H2>
 <P>
@@ -260,23 +260,36 @@
 <DIV ALIGN="CENTER">
 <H2>Copyright Notice for PHYLIP</H2></DIV>
 <P>
-The following copyright notice is intended to cover all source code, all
-documentation, and all executable programs of the PHYLIP package.
-<P>
-&#169; Copyright 1980-2013.  University of Washington.  All
-rights reserved.  Permission is granted to reproduce, perform, and modify
-these programs and documentation files.  Permission is granted to distribute
-or provide access to these
-programs provided that this copyright notice is not removed, the programs are
-not integrated with or called by any product or service that generates
-revenue, and that your distribution of these documentation files and programs
-are free.  Any modified
-versions of these materials that are distributed or accessible shall indicate
-that they are based on these programs.  Institutions of higher education are
-granted permission to distribute this material to their students and staff
-for a fee to recover distribution costs.  Permission requests for any other
-distribution of these programs should be directed to <TT>&nbsp;license<!deathtospam>&nbsp;(at)&nbsp;<!deathtospam>u.washington.edu&nbsp;</TT>.
-<BR>
+The following copyright notice given below is intended to cover all source code, all
+documentation, and all executable programs of the PHYLIP package.  This is
+a "BSD 2-Clause License" which is open source.  It is not a GNU license and
+does not insist that other materials distributed with PHYLIP be under a similar
+license.
+<P>
+&#169; Copyright 1980-2014, Joseph Felsenstein<BR>
+All rights reserved.
+<P>
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+<P>
+1. Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.
+<P>
+2. Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation
+and/or other materials provided with the distribution.
+<P>
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+<P>
 </TD></TR></TABLE></DIV>
 
 <BR>
@@ -1431,7 +1444,7 @@
 <P>
 <TABLE><TR><TD BGCOLOR=white>
 <PRE>
-DNA parsimony algorithm, version 3.7a
+DNA parsimony algorithm, version 3.695
 
 Setting for this run:
   U                 Search for best tree?  Yes
@@ -3532,7 +3545,7 @@
 instructions will work for it.
 <P>
 After you have finished unpacking the Documentation and Source Code
-archive, you will find that you have created a folder <TT>phylip-3.7a</TT>
+archive, you will find that you have created a folder <TT>phylip-3.6</TT>
 in which there are three
 folders, called <TT>exe</TT>, <TT>src</TT>, and <TT>doc</TT>.  
 There is also an HTML web page, <TT>phylip.html</TT>.  The <TT>exe</TT>
@@ -3595,7 +3608,7 @@
 by <TT>gcc</TT>.  You would then need to edit the Makefile to reflect this
 (see below for comments on that process).
 <P>
-A typical Unix or Linux installation would put the directory <TT>phylip-3.7a</TT>
+A typical Unix or Linux installation would put the directory <TT>phylip-3.6</TT>
 in <TT>/usr/local</TT>.  The name of the executables directory <TT>EXEDIR</TT>
 could be changed to be <TT>/usr/local/bin</TT>, so that the <TT>make install</TT>
 command puts the executables there.  If the users have <TT>/usr/local/bin</TT>
@@ -3708,7 +3721,7 @@
 "fred" on a Windows xp system, and have extracted our self-extracting
 archive of the Sources and Documentation files onto your desktop,
 you will want to change folders by typing the command
- <tt>&nbsp;&nbsp;cd C:/"Documents and Settings"/fred/phylip3.7a&nbsp;&nbsp;</tt>
+ <tt>&nbsp;&nbsp;cd C:/"Documents and Settings"/fred/phylip3.6&nbsp;&nbsp;</tt>
 <P>
 <LI> Make sure that there is a folder there called <tt>exe</tt> as well as
 one called <tt>src</tt>.  The former is where the executables will be
@@ -4040,7 +4053,7 @@
 <A NAME="vax"><H3>VMS VAX systems</H3></a>
 <P>
 VMS VAX systems have almost disappeared, so
-we have not tried to compile version 3.7a on an OpenVMS system.  The
+we have not tried to compile version 3.695 on an OpenVMS system.  The
 following instructions should work.
 On the OpenVMS operating system with DEC VAX VMS C the programs will compile
 without alteration.  The commands for compiling a typical program
@@ -4330,7 +4343,7 @@
 There is no executable program
 named <TT>PHYLIP</TT> in the PHYLIP package!  But in some cases
 (especially the Windows distribution) there is a file called
-<TT>phylip-3.7a.exe</TT>.
+<TT>phylip-3.695.exe</TT>.
 That file is an archive of documentation and source code.  Once you have
 run it and extracted the files in it, so that they are in the folder,
 running it again will just do the extraction again, which is unnecessary.
@@ -4749,7 +4762,7 @@
 writing?"</STRONG> 
 <DD>One way is like this:
 <P>
-Felsenstein, J.  2009.  PHYLIP (Phylogeny Inference Package) version 3.7a.
+Felsenstein, J.  2009.  PHYLIP (Phylogeny Inference Package) version 3.695.
 <I>Distributed by the author.  Department of Genome Sciences, University of
 Washington, Seattle.</I>
 <P>

=== modified file 'doc/mix.html'
--- doc/mix.html	2009-09-11 08:00:10 +0000
+++ doc/mix.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,15 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Mix - Mixed method discrete characters parsimony</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2008 by the University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 Mix is a general parsimony program which carries out the Wagner and
 Camin-Sokal parsimony methods in mixture, where each character can have

=== modified file 'doc/move.html'
--- doc/move.html	2009-09-11 08:00:10 +0000
+++ doc/move.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,15 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Move - Interactive mixed method parsimony</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2008 by the University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 Move is an interactive parsimony program, inspired by Wayne Maddison and
 David Maddison's marvellous program MacClade, which was written for
@@ -55,7 +53,7 @@
 <TABLE><TR><TD BGCOLOR=white>
 <PRE>
 
-Interactive mixed parsimony algorithm, version 3.69
+Interactive mixed parsimony algorithm, version 3.696
 
 Settings for this run:
   X                         Use Mixed method?  No

=== modified file 'doc/neighbor.html'
--- doc/neighbor.html	2013-08-07 22:17:03 +0000
+++ doc/neighbor.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,15 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Neighbor -- Neighbor-Joining and UPGMA methods</H1>
 </DIV>
 <P>
-&#169; Copyright 1991-2012 by the University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1991-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 This program implements the Neighbor-Joining method of Saitou and Nei (1987)
 and the UPGMA method of clustering.  The program was written by Mary Kuhner

=== modified file 'doc/pars.html'
--- doc/pars.html	2009-09-11 08:00:10 +0000
+++ doc/pars.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,15 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Pars - Discrete character parsimony</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2008 by the University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 Pars is a general parsimony program which carries out the Wagner
 parsimony method with multiple states.  Wagner parsimony

=== modified file 'doc/penny.html'
--- doc/penny.html	2009-09-11 08:00:10 +0000
+++ doc/penny.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,15 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Penny - Branch and bound to find<BR>all most parsimonious trees</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2008 by the University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 Penny is a program that will find all of the most parsimonious trees
 implied by your data.  It does so not by examining all possible trees,
@@ -253,7 +251,7 @@
 <TABLE><TR><TD BGCOLOR=white>
 <PRE>
 
-Penny algorithm, version 3.69
+Penny algorithm, version 3.696
  branch-and-bound to find all most parsimonious trees
 
 Settings for this run:

=== modified file 'doc/proml.html'
--- doc/proml.html	2009-09-11 08:00:10 +0000
+++ doc/proml.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,15 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Proml -- Protein Maximum Likelihood program</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2008 by the University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 This program implements the maximum likelihood method for protein
 amino acid sequences.
@@ -127,7 +125,7 @@
 <TABLE><TR><TD BGCOLOR=white>
 <PRE>
 
-Amino acid sequence Maximum Likelihood method, version 3.69
+Amino acid sequence Maximum Likelihood method, version 3.696
 
 Settings for this run:
   U                 Search for best tree?  Yes

=== modified file 'doc/promlk.html'
--- doc/promlk.html	2009-09-11 08:00:10 +0000
+++ doc/promlk.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,15 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Promlk -- Protein maximum likelihood program<BR>with molecular clock</H1>
 </DIV>
 <P>
-&#169; Copyright 2000-2008 by the University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 2000-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 This program implements the maximum likelihood method for protein amino
 acid sequences under the constraint that the trees estimated must be

=== modified file 'doc/protdist.html'
--- doc/protdist.html	2009-09-11 08:00:10 +0000
+++ doc/protdist.html	2015-04-04 21:58:41 +0000
@@ -9,7 +9,7 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
@@ -17,10 +17,8 @@
 from protein sequences</H1>
 </DIV>
 <P>
-&#169; Copyright 1993, 2000-2008 by the University of Washington.  Permission
-is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1983, 2000-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 This program uses protein sequences to compute a distance matrix, under
 four different models of amino acid replacement. It can also

=== modified file 'doc/protpars.html'
--- doc/protpars.html	2009-09-11 08:00:10 +0000
+++ doc/protpars.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,15 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Protpars -- Protein Sequence Parsimony Method</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2008 by the University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 </EM>
 <P>

=== modified file 'doc/restdist.html'
--- doc/restdist.html	2009-09-11 08:00:10 +0000
+++ doc/restdist.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,15 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Restdist -- Program to compute distance matrix<BR>from restriction sites or fragments</H1>
 </DIV>
 <P>
-&#169; Copyright 2000-2008 by the University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 2000-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 Restdist reads the same restriction sites format as Restml and
 computes a restriction sites distance.  It can also compute a restriction

=== modified file 'doc/restml.html'
--- doc/restml.html	2009-09-11 08:00:10 +0000
+++ doc/restml.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,15 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Restml -- Restriction sites Maximum Likelihood program</H1>
 </DIV>
 <P>
-&#169; Copyright 1986-2008 by The University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 This program implements a maximum likelihood method for restriction sites
 data (not restriction fragment data).  This program is one of the slowest 

=== modified file 'doc/retree.html'
--- doc/retree.html	2009-09-11 08:00:10 +0000
+++ doc/retree.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,15 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Retree -- Interactive Tree Rearrangement</H1>
 </DIV>
 <P>
-&#169; Copyright 1993-2008 by The University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1993-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 Retree is a tree editor.  It reads in a tree,
 or allows the user to construct one, and

=== modified file 'doc/seqboot.html'
--- doc/seqboot.html	2009-09-11 08:00:10 +0000
+++ doc/seqboot.html	2015-04-04 21:58:41 +0000
@@ -10,7 +10,7 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
@@ -19,10 +19,8 @@
 Gene Frequency or Character Data</H1>
 </DIV>
 <P>
-&#169; Copyright 1991-2008 by the University of Washington.
-Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1991-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 Seqboot is a general bootstrapping and data set translation tool.  It is intended to allow you to
 generate multiple data sets that are resampled versions of the input data

=== modified file 'doc/sequence.html'
--- doc/sequence.html	2009-09-11 08:00:10 +0000
+++ doc/sequence.html	2015-04-04 21:58:41 +0000
@@ -10,16 +10,14 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <DIV ALIGN=CENTER>
 <H1>Molecular Sequence Programs</H1>
 </DIV>
 <P>
-(c) Copyright 1986-2008 by The University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 1986-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 These programs estimate phylogenies from protein
 sequence or nucleic acid sequence data.  Protpars uses a parsimony method 

=== modified file 'doc/treedist.html'
--- doc/treedist.html	2009-09-11 08:00:10 +0000
+++ doc/treedist.html	2015-04-04 21:58:41 +0000
@@ -10,17 +10,15 @@
 </HEAD>
 <BODY BGCOLOR="#ccffff">
 <DIV ALIGN=RIGHT>
-version 3.69
+version 3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>
 <H1>Treedist -- distances between trees</H1>
 </DIV>
 <P>
-&#169; Copyright 2000-2008 by The University of
-Washington.  Written by Joseph Felsenstein.  Permission is granted to copy 
-this document provided that no fee is charged for it and that this copyright 
-notice is not removed. 
+&#169; Copyright 2000-2014 by Joseph Felsenstein. All rights reserved.
+License terms <a href="main.html#copyright">here</a>.
 <P>
 This program computes distances between trees.  Two distances are computed,
 the Branch Score Distance of Kuhner and Felsenstein (1994), and

=== modified file 'phylip.html'
--- phylip.html	2006-09-01 23:30:58 +0000
+++ phylip.html	2015-04-04 21:58:41 +0000
@@ -11,7 +11,7 @@
 <BODY BGCOLOR="#ccffff">
 <P>
 <DIV ALIGN=RIGHT>
-v3.6
+v3.696
 </DIV>
 <P>
 <DIV ALIGN=CENTER>

=== modified file 'src/COPYRIGHT'
--- src/COPYRIGHT	2013-08-07 22:17:03 +0000
+++ src/COPYRIGHT	2015-04-04 21:58:41 +0000
@@ -3,15 +3,27 @@
 The following copyright notice is intended to cover all source code, all
 documentation, and all executable programs of the PHYLIP package.
 
-© Copyright 1980-2012 by the University of Washington. All rights reserved.
-Permission is granted to reproduce, perform, and modify these programs and
-documentation files. Permission is granted to distribute or provide access to
-these programs provided that this copyright notice is not removed, the programs
-are not integrated with or called by any product or service that generates
-revenue, and that your distribution of these documentation files and programs
-are free. Any modified versions of these materials that are distributed or
-accessible shall indicate that they are based on these programs. Institutions
-of higher education are granted permission to distribute this material to their
-students and staff for a fee to recover distribution costs. Permission requests
-for any other distribution of these program should be directed to  license (at)
-u.washington.edu . 
+Copyright (c) 1980-2014, Joseph Felsenstein
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation
+and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+

=== removed file 'src/Makefile.cyg'
--- src/Makefile.cyg	2013-08-07 22:17:03 +0000
+++ src/Makefile.cyg	1970-01-01 00:00:00 +0000
@@ -1,741 +0,0 @@
-# Makefile
-#
-# Gnu Cygwin Makefile for PHYLIP 3.695
-# This builds the Windows executables
-
-PACKAGE=phylip
-VERSION=3.695
-
-# We use GNU's version of the make utility. It may be called "gmake" on
-# your system.
-#
-# If you're using a RedHat Linux system with default locations for 
-# gcc libraries, you probably don't need to change anything. You might
-# might change the first noncomment statement below to redefine $(EXEDIR)
-# if you'd like your executables installed in a different location than
-# our default.
-#
-# Users with systems that differ substantially from ours may need to set
-# the following variables: $(CC) $(CFLAGS) $(DFLAGS) $(LIBS) $(S)
-#
-# When uncompressed and extracted, the tar archive phylip-3.6x.tar.gz 
-# produces the following directory structure:
-#
-#   phylip-3.6x/source -- the source code, including this Makefile
-#   phylip-3.6x/exe -- executables, changed by changing $(EXEDIR) value
-#   phylip-3.6x/doc -- html documentation
-#
-#  To use the PHYLIP v3.6 Makefile, type from the phylip-3.6x/src directory:
-#      cp Makefile Makefile.unix
-#      cp Makefile.cyg Makefile
-#  and then do one of the following. (You can skip the copying steps
-#  above and use "make -f Makefile.cyg ..." instead if you like.)
-#
-#      make install         to compile the whole package and install
-#                           the executables in $(EXEDIR), and then
-#                           remove the object files to save space
-#
-#      make all             to compile the whole package but not install it
-#                           or remove the object files. 
-#
-#      make put             to move the executables into $(EXEDIR)
-#
-#      make clean           to remove all object files and executables from the
-#                           current directory
-#
-#      make dnaml           to compile and link one program, (in this example,
-#                           DnaML) and leave the executable and object files
-#                           in the current directory (where the source code is).
-#                           You will have to move the executable into the
-#                           executables directory (e.g. "mv dnaml ../exe")
-#                           Note that the program name should be lower case.
-# 
-# ----------------------------------------------------------------------------
-#  (Starting here is the section where you may want to change things)
-# ----------------------------------------------------------------------------
-#
-# the following specifies the directory where the executables will be placed
-EXEDIR  = ../exe
-#
-# ----------------------------------------------------------------------------
-#
-# The following statements set these variables:
-#
-#    CC     -- the name (and, optionally, location) of your C compiler
-#    CFLAGS -- compiler directives needed to compile most programs
-#    DFLAGS -- compiler directives needed to compile draw programs
-#    LIBS   -- non-default system libraries needed to compile most programs
-#    S  -- non-default system libraries needed to compile draw programs
-#
-# We've provided a set of possible values for each variable.
-#
-# The value used is the one without a "#" at the beginning of the line.
-#
-# To try an alternate value, make sure the one you want has no "#"
-# as its first character and that all other possibilities have "#" for
-# their first character.
-#
-# Advanced users may need to further edit one of the alternatives in
-# order to correctly compile on their system.
-#
-# ----------------------------------------------------------------------------
-#
-# The next two assignments are the invocations of the compiler
-#
-# This one specifies the default cygwin "cc" C compiler
-# It requires cygwin1.dll to be in the execution directory
-#CC		= cc
-#
-# This one uses the mingw w64 compiler which does not require any extra dll's
-# The full path makes this a bit touchy, so if the compile crashes you'll need 
-# to find where the mingw32 compiler had been moved
-CC		= /usr/bin/i686-w64-mingw32-gcc-4.5.3.exe
-#
-#  To use GCC instead:
-#CC        = gcc
-#
-# ----------------------------------------------------------------------------
-#
-# This is the CFLAGS statement. It specifies compiler behavior.
-CFLAGS  = -MNO-CYGWIN -DWIN32 -O3 -fomit-frame-pointer -ffast-math
-#CFLAGS  = -fomit-frame-pointer -ffast-math
-#
-# This is the DFLAGS statement. It specifies compiler behavior for the
-# programs drawgram and drawtree.
-DFLAGS  = -MNO-CYGWIN -lgdi32
-#DFLAGS  =  
-#
-# ----------------------------------------------------------------------------
-#
-# The cygwin compile automatically pics up the libraries we need, so
-# the $(LIBS) variable is empty
-LIBS    =
-#
-#S	=	$(LIBS) -luser32 -lgdi32
-#
-# ----------------------------------------------------------------------------
-#  (After this point there should not be any reason to change anything)
-# ----------------------------------------------------------------------------
-
-WINDRES		= windres
-#
-#
-# the list of programs
-# draw programs are listed last since they are the most likely to cause
-# compilation or linking problems
-
-PROGS   =		clique.exe \
-				consense.exe \
-				contml.exe \
-				contrast.exe \
-				dnacomp.exe \
-				dnadist.exe \
-				dnainvar.exe \
-				dnaml.exe \
-				dnamlk.exe \
-				dnamove.exe \
-				dnapars.exe \
-				dnapenny.exe \
-				dolmove.exe \
-				dollop.exe \
-				dolpenny.exe \
-				drawgram.exe \
-				drawtree.exe \
-				factor.exe \
-				fitch.exe \
-				gendist.exe \
-				kitsch.exe \
-				mix.exe \
-				move.exe \
-				neighbor.exe \
-				pars.exe \
-				penny.exe \
-				proml.exe \
-				promlk.exe \
-				protdist.exe \
-				protpars.exe \
-				restdist.exe \
-				restml.exe \
-				retree.exe \
-				seqboot.exe \
-				treedist.exe 
-
-DYLIBS    =     drawgram.dll \
-                drawtree.dll
-                
-JARS    =       javajars/DrawGram.jar \
-                javajars/DrawTree.jar \
-                javajars/DrawGramJava.bat \
-                javajars/DrawTreeJava.bat \
-                javajars/DrawGramJava.exe \
-                javajars/DrawTreeJava.exe
-#
-# general commands
-#
-
-#  The first target it executed if you just type "make".  It tells you how to
-#  use the Makefile.
-#
-help:
-	@echo ""
-	@echo " To use the PHYLIP v$(VERSION) Makefile, type"
-	@echo "     make install       to compile the whole package and install"
-	@echo "                          the executables in $(EXEDIR), and then"
-	@echo "                          remove the object files to save space"
-	@echo "     make all           to compile the whole package but not install it"
-	@echo "                          or remove the object files"
-	@echo "     make put           to move the executables into $(EXEDIR)"
-	@echo "     make clean         to remove all object files and executables from the"
-	@echo "                          current directory"
-	@echo "     make dnaml         to compile and link one program, (in this example,"
-	@echo "                          Dnaml) and leave the executable and object files"
-	@echo "                          in the current directory (where the source code is)."
-	@echo "                          You will have to move the executable into the"
-	@echo "                          executables directory (e.g. \"mv dnaml $(EXEDIR)\")"
-	@echo "                          Note that the program name should be lower case."
-	@echo " "
-
-# The following is so that a command like
-# make dnaml 
-# will actually do something usefull
-.PHONY :    clique consense contml contrast dnacomp dnadist \
-                   dnainvar dnaml dnamlk dnamove dnapars dnapenny \
-                   dolmove dollop dolpenny factor fitch gendist kitsch \
-                   mix move neighbor pars penny proml promlk protdist \
-                   protpars restdist restml retree seqboot treedist \
-                   drawgram drawtree
- 
-clique: clique.exe
-consense: consense.exe
-contml: contml.exe
-contrast: contrast.exe
-dnacomp: dnacomp.exe
-dnadist: dnadist.exe
-dnainvar: dnainvar.exe
-dnaml: dnaml.exe
-dnamlk: dnamlk.exe
-dnamove: dnamove.exe
-dnapars: dnapars.exe
-dnapenny: dnapenny.exe
-dolmove: dolmove.exe
-dollop: dollop.exe
-dolpenny: dolpenny.exe
-drawgram: drawgram.exe
-drawtree: drawtree.exe
-factor: factor.exe
-fitch: fitch.exe
-gendist: gendist.exe
-kitsch: kitsch.exe
-mix: mix.exe
-move: move.exe
-neighbor: neighbor.exe
-pars: pars.exe
-penny: penny.exe
-proml: proml.exe
-promlk: promlk.exe
-protdist: protdist.exe
-protpars: protpars.exe
-restdist: restdist.exe
-restml: restml.exe
-retree: retree.exe
-seqboot: seqboot.exe
-treedist: treedist.exe
-
-introduce:
-	@echo "Building PHYLIP version $(VERSION)"
-
-all:        introduce $(PROGS) $(DYLIBS)
-	@echo "Finished compiling."
-	@echo ""
-
-install:        all put clean
-	@echo "Done."
-	@echo ""
-
-put:
-# removed because cygwin does not like it
-#	@echo "Stripping executables to save space"
-#	strip --strip-all *.exe 
-	@echo "Installing PHYLIP v$(VERSION) binaries in $(EXEDIR)"
-	@mkdir -p $(EXEDIR)
-	@cp $(PROGS) $(EXEDIR)
-	@echo "Installing dynamic libraries in $(EXEDIR)"
-	@cp $(DYLIBS) $(EXEDIR)
-	@echo "Installing jar files in $(EXEDIR)"
-	@cp $(JARS) $(EXEDIR)
-	@echo "Installing font files in $(EXEDIR)"
-	@cp font* $(EXEDIR)
-	mkdir $(EXEDIR)/testdata
-	@echo "Copying testdata files to $(EXEDIR)/testdata..."
-	for i in $(TESTDIR); do \
-      mkdir $(EXEDIR)/testdata/$$i; \
-      cp src/testdata/$$i/*.txt $(EXEDIR)/testdata/$$i; \
-    done
-	@echo "Finished installation."
-	@echo ""
-
-clean:
-	@echo "Removing object files to save space"
-	@rm -f *.o
-	@rm -f *.res
-	@rm -f *.dll
-	@echo "Finished removing object files.  Now will remove"
-	@echo "executable files from the current directory, but not from the"
-	@echo "executables directory.  (If some are not here, the makefile"
-	@echo "will terminate with an error message but this is not a problem)"
-	@echo ""
-	@echo "Removing executables from this directory"
-	@rm -f $(PROGS)
-	@echo "Finished cleanup."
-	@echo ""
-
-#
-# compile object files shared between programs
-# (make's implicit rule for %.o will take care of these)
-#
-
-phylip.o:     phylip.c phylip.h
-seq.o:        phylip.h seq.h
-disc.o:       phylip.h disc.h
-discrete.o:   phylip.h discrete.h
-dollo.o:      phylip.h dollo.h
-wagner.o:     phylip.h wagner.h
-dist.o:       phylip.h dist.h
-cont.o:       phylip.h cont.h
-mlclock.o:    phylip.h mlclock.h
-moves.o:      phylip.h moves.h
-printree.o:   phylip.h printree.h
-
-
-#
-# compile the individual programs
-#
-
-clique.o:       clique.c disc.h phylip.h
-
-clique.exe:       clique.o disc.o phylip.o clique.res 
-	$(CC) $(CFLAGS) clique.o disc.o phylip.o clique.res $(LIBS) -o clique
-
-cons.o:         cons.c cons.h phylip.h 
-
-consense.o:     consense.c cons.h phylip.h
-
-consense.exe:     consense.o phylip.o cons.o consense.res
-	$(CC) $(CFLAGS) consense.o phylip.o cons.o consense.res $(LIBS) -o consense
-
-contml.o:       contml.c cont.h phylip.h
-
-contml.exe:       contml.o cont.o phylip.o contml.res
-	$(CC) $(CFLAGS) contml.o cont.o phylip.o contml.res $(LIBS) -o contml
-
-contrast.o:       contrast.c cont.h phylip.h
-
-contrast.exe:       contrast.o contrast.res cont.o phylip.o
-	$(CC) $(CFLAGS) contrast.o cont.o phylip.o contrast.res $(LIBS) -o contrast
-
-dnacomp.o:      dnacomp.c seq.h phylip.h
-
-dnacomp.exe:      dnacomp.o seq.o phylip.o dnacomp.res
-	$(CC) $(CFLAGS) dnacomp.o seq.o phylip.o dnacomp.res $(LIBS) -o dnacomp
-
-dnadist.o:      dnadist.c seq.h phylip.h
-
-dnadist.exe:      dnadist.o seq.o phylip.o dnadist.res
-	$(CC) $(CFLAGS) dnadist.o seq.o phylip.o dnadist.res $(LIBS) -o dnadist
-
-dnainvar.o:      dnainvar.c seq.h phylip.h
-
-dnainvar.exe:      dnainvar.o seq.o phylip.o dnainvar.res
-	$(CC) $(CFLAGS) dnainvar.o seq.o phylip.o dnainvar.res $(LIBS) -o dnainvar
-
-dnaml.o:      dnaml.c seq.h phylip.h
-
-dnaml.exe:      dnaml.o seq.o phylip.o dnaml.res
-	$(CC) $(CFLAGS) dnaml.o seq.o phylip.o dnaml.res $(LIBS) -o dnaml
-
-dnamlk.o: dnamlk.c seq.h phylip.h mlclock.h printree.h
-
-dnamlk.exe:      dnamlk.o seq.o phylip.o mlclock.o printree.o dnamlk.res
-	$(CC) $(CFLAGS) dnamlk.o seq.o phylip.o mlclock.o printree.o dnamlk.res $(LIBS) -o dnamlk
-
-dnamove.o:	dnamove.c seq.h moves.h phylip.h
-
-dnamove.exe:	dnamove.o seq.o moves.o phylip.o dnamove.res
-	$(CC) $(CFLAGS) dnamove.o seq.o moves.o phylip.o dnamove.res $(LIBS) -o dnamove
-
-dnapenny.o:      dnapenny.c seq.h phylip.h
-
-dnapenny.exe:      dnapenny.o seq.o phylip.o dnapenny.res
-	$(CC) $(CFLAGS) dnapenny.o seq.o phylip.o dnapenny.res $(LIBS) -o dnapenny
-
-dnapars.o:      dnapars.c seq.h phylip.h
-
-dnapars.exe:      dnapars.o seq.o phylip.o dnapars.res
-	$(CC) $(CFLAGS) dnapars.o seq.o phylip.o dnapars.res $(LIBS) -o dnapars
-
-dolmove.o:       dolmove.c disc.h moves.h dollo.h phylip.h
-
-dolmove.exe:       dolmove.o disc.o moves.o dollo.o phylip.o dolmove.res
-	$(CC) $(CFLAGS) dolmove.o disc.o moves.o dollo.o phylip.o dolmove.res $(LIBS) -o dolmove
-
-dollop.o:       dollop.c disc.h dollo.h phylip.h
-
-dollop.exe:       dollop.o disc.o dollo.o phylip.o dollop.res
-	$(CC) $(CFLAGS) dollop.o disc.o dollo.o phylip.o dollop.res $(LIBS) -o dollop
-
-dolpenny.o:       dolpenny.c disc.h dollo.h phylip.h
-
-dolpenny.exe:       dolpenny.o disc.o dollo.o phylip.o dolpenny.res
-	$(CC) $(CFLAGS) dolpenny.o disc.o dollo.o phylip.o dolpenny.res $(LIBS) -o dolpenny
-	
-draw.o:   draw.c draw.h phylip.h 
-	$(CC) $(CFLAGS) -c draw.c
-
-draw2.o:   draw2.c draw.h phylip.h 
-	$(CC) $(CFLAGS) -c draw2.c
-
-drawgram.o:     drawgram.c draw.h phylip.h
-	$(CC) $(CFLAGS) -c drawgram.c
-
-drawgram.exe:     drawgram.o draw.o draw2.o phylip.o drawgram.res
-	$(CC) $(CFLAGS) drawgram.o draw.o draw2.o phylip.o drawgram.res $(LIBS) -o drawgram
-
-drawtree.o:     drawtree.c draw.h phylip.h
-	$(CC) $(CFLAGS) -c drawtree.c
-
-drawtree.exe:     drawtree.o draw.o draw2.o phylip.o drawtree.res
-	$(CC) $(CFLAGS) drawtree.o draw.o draw2.o phylip.o drawtree.res	$(LIBS) -o drawtree		
-
-# needed by java	
-phylipDlib.o:     phylip.c phylip.h
-	$(CC) $(DFLAGS) -c phylip.c -o phylipDlib.o
-	
-drawDlib.o:   draw.c draw.h phylip.h 
-	$(CC) $(DFLAGS) -c draw.c -o drawDlib.o
-
-draw2Dlib.o:   draw2.c draw.h phylip.h 
-	$(CC) $(DFLAGS) -c draw2.c -o draw2Dlib.o
-
-drawgramDlib.o:     drawgram.c draw.h phylip.h
-	$(CC) $(DFLAGS) -c drawgram.c -o drawgramDlib.o
-
-drawtreeDlib.o:     drawtree.c draw.h phylip.h
-	$(CC) $(DFLAGS) -c drawtree.c -o drawtreeDlib.o
-
-drawgram.dll:     drawgramDlib.o drawDlib.o draw2Dlib.o phylipDlib.o
-	$(CC) $(DFLAGS) -shared -o drawgram.dll -shared drawgramDlib.o drawDlib.o draw2Dlib.o phylipDlib.o
-
-drawtree.dll:     drawtreeDlib.o drawDlib.o draw2Dlib.o phylipDlib.o
-	$(CC) $(DFLAGS)  -shared -o drawtree.dll -shared drawtreeDlib.o drawDlib.o draw2Dlib.o phylipDlib.o			
-# end Java interface stuff	
-
-factor.o:       factor.c phylip.h
-
-factor.exe:       factor.o phylip.o factor.c factor.res
-	$(CC) $(CFLAGS) factor.o phylip.o factor.res $(LIBS) -o factor
-
-fitch.o:        fitch.c dist.h phylip.h
-
-fitch.exe:        fitch.o dist.o phylip.o fitch.res
-	$(CC) $(CFLAGS) fitch.o dist.o phylip.o fitch.res $(LIBS) -o fitch
-
-gendist.o:      gendist.c phylip.h
-
-gendist.exe:      gendist.o phylip.o gendist.res
-	$(CC) $(CFLAGS) gendist.o phylip.o gendist.res $(LIBS) -o gendist
-
-kitsch.o:        kitsch.c dist.h phylip.h
-
-kitsch.exe:        kitsch.o dist.o phylip.o kitsch.res
-	$(CC) $(CFLAGS) kitsch.o dist.o phylip.o kitsch.res $(LIBS) -o kitsch
-
-mix.o:        mix.c disc.h wagner.h phylip.h
-
-mix.exe:        mix.o disc.o wagner.o phylip.o mix.res
-	$(CC) $(CFLAGS) mix.o disc.o wagner.o phylip.o mix.res $(LIBS) -o mix
-
-move.o:        move.c disc.h moves.h wagner.h phylip.h
-
-move.exe:        move.o disc.o moves.o wagner.o phylip.o move.c move.res
-	$(CC) $(CFLAGS) move.o disc.o moves.o wagner.o phylip.o move.res $(LIBS) -o move
-
-neighbor.o:        neighbor.c dist.h phylip.h
-
-neighbor.exe:        neighbor.o dist.o phylip.o neighbor.res 
-	$(CC) $(CFLAGS) neighbor.o dist.o phylip.o neighbor.res $(LIBS) -o neighbor
-
-pars.o:   pars.c discrete.c discrete.h phylip.h
-
-pars.exe: pars.o discrete.o phylip.o pars.res
-	$(CC) $(CFLAGS) pars.o discrete.o phylip.o pars.res $(LIBS) -o pars
-
-penny.o:  penny.c disc.h wagner.h phylip.h
-
-penny.exe:  penny.o disc.o wagner.o phylip.o penny.res
-	$(CC) $(CFLAGS) penny.o disc.o wagner.o  phylip.o penny.res $(LIBS) -o penny
-
-proml.o:      proml.c seq.h phylip.h
-
-proml.exe:      proml.o seq.o phylip.o proml.res
-	$(CC) $(CFLAGS) proml.o seq.o phylip.o proml.res $(LIBS) -o proml
-
-promlk.o: seq.h phylip.h mlclock.h printree.h
-
-promlk.exe: promlk.o seq.o phylip.o mlclock.o printree.o promlk.res
-	$(CC) $(CFLAGS) promlk.o seq.o phylip.o mlclock.o printree.o promlk.res $(LIBS) -o promlk
-
-protdist.o:      protdist.c seq.h phylip.h
-
-protdist.exe:      protdist.o seq.o phylip.o protdist.res
-	$(CC) $(CFLAGS) protdist.o seq.o phylip.o protdist.res $(LIBS) -o protdist
-
-protpars.o: protpars.c seq.h phylip.h
-
-protpars.exe: protpars.o seq.o phylip.o protpars.res
-	$(CC) $(CFLAGS) protpars.o seq.o phylip.o protpars.res $(LIBS) -o protpars
-
-restdist.o: restdist.c seq.h phylip.h
-
-restdist.exe: restdist.o restdist.res seq.o phylip.o restdist.res
-	$(CC) $(CFLAGS) restdist.o seq.o phylip.o restdist.res $(LIBS) -o restdist
-
-restml.o: restml.c seq.h phylip.h
-
-restml.exe: restml.o seq.o phylip.o restml.res
-	$(CC) $(CFLAGS) restml.o seq.o phylip.o restml.res $(LIBS) -o restml
-
-retree.o:       retree.c moves.h phylip.h
-
-retree.exe:       retree.o moves.o phylip.o retree.res
-	$(CC) $(CFLAGS) retree.o moves.o phylip.o retree.res $(LIBS) -o retree
-
-seqboot.o:      seqboot.c phylip.h
-
-seqboot.exe:      seqboot.o seq.o phylip.o seqboot.res
-	$(CC) $(CFLAGS) seqboot.o seq.o phylip.o seqboot.res $(LIBS) -o seqboot
-
-treedist.o:     treedist.c cons.c cons.h phylip.h
-
-treedist.exe:     treedist.o phylip.o cons.o treedist.res
-	$(CC) $(CFLAGS) treedist.o cons.o phylip.o treedist.res $(LIBS) -o treedist
-
-%.res: icons/%.rc
-	$(WINDRES) $< -O coff -o $@
-
-#
-# Targets for making the Windows distribution archives
-#
-
-DISTDIR=$(PACKAGE)-$(VERSION)
-ASCII_EXT= .c .h .html
-
-SFX_STUB=SFXWiz32.exe
-
-DIST_COMMON = ../phylip.html 
-
-DOC_DIR = ../doc
-
-IMG_DIR = ../doc/images
-
-TEST_DIR = ../src/testdata
-
-DOCS= clique.html consense.html contchar.html contml.html \
-      contrast.html discrete.html distance.html dnacomp.html \
-      dnadist.html dnainvar.html dnaml.html dnamlk.html \
-      dnamove.html dnapars.html dnapenny.html dollop.html \
-      dolmove.html dolpenny.html drawgram.html draw.html \
-      drawtree.html factor.html fitch.html gendist.html \
-      kitsch.html main.html mix.html move.html \
-      neighbor.html pars.html penny.html proml.html \
-      promlk.html protdist.html protpars.html restdist.html \
-      restml.html retree.html seqboot.html sequence.html \
-      treedist.html phylip.gif
-      
-IMAGES= DrawGramCat.png DrawGramControls.png \
-     DrawTreeCat.png DrawTreeControls.png \
-     InputTree.png
-
-SOURCES=  Makefile.cyg Makefile.osx Makefile.unx \
-          clique.c cons.c consense.c cons.h cont.c \
-          cont.h contml.c contrast.c disc.c disc.h discrete.c discrete.h dist.c \
-          dist.h dnacomp.c dnadist.c dnainvar.c dnaml.c dnamlk.c dnamove.c \
-	        dnapars.c dnapenny.c dollo.c dollo.h dollop.c dolmove.c dolpenny.c \
-	        draw2.c draw.c draw.h drawgram.c drawtree.c\
-	        factor.c fitch.c gendist.c \
-	        interface.c interface.h io.h kitsch.c macface.c macface.h mix.c move.c \
-	        moves.c moves.h neighbor.c newmove.c pars.c penny.c \
-	        phylip.c phylip.h proml.c promlk.c protdist.c protpars.c restdist.c \
-	        restml.c retree.c seqboot.c seq.c seq.h treedist.c wagner.c wagner.h \
-	        mlclock.c mlclock.h printree.c printree.h font1 font2 font3 font4 font5 font6
-	 
-
-ICONS=  icons/boot.ico icons/clique.ico icons/clique.rc icons/clique.rcb icons/consense.ico \
-        icons/consense.rc icons/consense.rcb icons/contml.ico icons/contml.rc icons/contml.rcb \
-        icons/contrast.ico icons/contrast.rc icons/contrast.rcb icons/disc.ico icons/dist.ico icons/dna.ico \
-        icons/dnacomp.rc icons/dnacomp.rcb icons/dnadist.rc icons/dnadist.rcb icons/dnainvar.rc \
-        icons/dnainvar.rcb icons/dnaml.rc icons/dnaml.rcb icons/dnamlk.rc icons/dnamlk.rcb icons/dnamove.rc \
-        icons/dnamove.rcb icons/dnapars.rc icons/dnapars.rcb icons/dnapenny.rc icons/dnapenny.rcb \
-        icons/dollo.ico icons/dollop.rc icons/dollop.rcb icons/dolmove.rc icons/dolmove.rcb \
-        icons/dolpenny.rc icons/dolpenny.rcb icons/drawgram.ico icons/drawgram.rc icons/drawgram.rcb \
-        icons/drawtree.ico icons/drawtree.rc icons/drawtree.rcb icons/factor.rc icons/factor.rcb \
-        icons/fitch.rc icons/fitch.rcb icons/gendist.ico icons/gendist.rc icons/gendist.rcb icons/kitsch.rc \
-        icons/kitsch.rcb icons/mix.rc icons/mix.rcb icons/move.rc icons/move.rcb icons/neighbor.rc \
-        icons/neighbor.rcb icons/pars.rc icons/pars.rcb icons/penny.rc icons/penny.rcb icons/proml.rc \
-        icons/proml.rcb icons/promlk.rc icons/promlk.rcb icons/protdist.rc icons/protdist.rcb \
-        icons/protein.ico icons/protpars.rc icons/protpars.rcb icons/restdist.rc icons/restdist.rcb \
-        icons/restml.rc icons/restml.rcb icons/restrict.ico icons/retree.ico icons/retree.rc \
-        icons/retree.rcb icons/seqboot.rc icons/seqboot.rcb icons/treedist.ico icons/treedist.rc \
-        icons/treedist.rcb
-
-W_EXES =	dnacomp.exe dnadist.exe dnainvar.exe dnaml.exe dnamlk.exe \
-          dnamove.exe dnapars.exe dnapenny.exe proml.exe promlk.exe \
-          protdist.exe protpars.exe restdist.exe restml.exe seqboot.exe \
-          clique.exe consense.exe contml.exe contrast.exe dollop.exe \
-          dolmove.exe dolpenny.exe factor.exe \
-          fitch.exe font1 font2 font3 font4 font5 font6 gendist.exe \
-          kitsch.exe mix.exe move.exe neighbor.exe pars.exe penny.exe \
-          retree.exe treedist.exe
-
-TESTDIR=  clique consense contml contrast dnacomp \
-          dnadist dnainvar dnaml dnamlk dnamove dnapars dnapenny dollop \
-          dolmove dolpenny drawgram drawtree factor fitch gendist \
-          kitsch mix move neighbor pars penny proml promlk \
-          protdist protpars restdist restml retree seqboot  treedist
-      
-JAVAJAR=  javajars/DrawGram.jar javajars/DrawTree.jar \
-          javajars/DrawGramJava.bat javajars/DrawTreeJava.bat \
-          javajars/DrawGramJava.exe javajars/DrawTreeJava.exe \
-          javajars/DrawGramJava.unx javajars/DrawTreeJava.unx
-        
-JAVAEXE=  javajars/DrawGram.jar javajars/DrawTree.jar \
-          javajars/DrawGramJava.exe javajars/DrawTreeJava.exe \
-          drawgram.dll drawtree.dll
-
-.PHONY : phylipwdir phylipw.zip
-
-dists : dist sfx zips sfxs
-
-sfxs : phylipw.exe
-
-zips : phylipw.zip
-
-phylipw.exe : phylipw.zip
-	cat $(SFX_STUB) phylipw.zip > phylipw.exe \
-	  && chmod 755 phylipw.exe
-
-phylipw.zip : phylipwdir
-	@rm -f phylipw.zip
-	cd phylipw && zip -q -r ../phylipw.zip *
-	rm -rf phylipw
-
-phylipwdir : $(DOCS) $(SOURCES) $(ICONS)
-	rm -rf phylipw
-	mkdir phylipw
-	mkdir phylipw/$(DISTDIR)
-	mkdir phylipw/$(DISTDIR)/src
-	mkdir phylipw/$(DISTDIR)/doc
-	mkdir phylipw/$(DISTDIR)/doc/images
-	mkdir phylipw/$(DISTDIR)/exe
-	mkdir phylipw/$(DISTDIR)/src/icons
-	for i in $(DIST_COMMON) ; do \
-	  cp $$i phylipw/$(DISTDIR) ; \
-	done
-	for i in $(DOCS) ; do \
-	  cp DOC_DIR/$$i phylipw/$(DISTDIR)/doc ; \
-	done
-	for i in $(SOURCES) ; do \
-	  cp $$i phylipw/$(DISTDIR)/src ; \
-	done
-	for i in $(ICONS) ; do \
-	  cp $$i phylipw/$(DISTDIR)/src/icons ; \
-	done
-	@for i in $(ASCII_EXT) ; do \
-	  echo "Translating newline characters on *$$i..." ; \
-	  find phylipw -name "*$$i" \
-	    -exec sed -i -e 's/$$/\r/g' '{}' ';' ; \
-	done
-
-# not currently working
-#sfx : dist
-#	@echo "Creating self-extracting zip archive $(DISTDIR).exe"
-#	cat $(SFX_STUB) $(DISTDIR).zip > $(DISTDIR).exe \
-#	  && chmod 755 $(DISTDIR).exe
-
-dist : distdir
-	-rm -rf $(DISTDIR).zip
-	@echo "Creating ZIP archive $(DISTDIR).zip"
-	zip -q -r $(DISTDIR).zip $(DISTDIR)
-	rm -rf $(DISTDIR)
-        
-
-distdir : $(DIST_COMMON) $(SOURCES) $(ICONS) $(TESTDIR) $(JAVAJAR) $(DYLIBS)
-	-rm -rf $(DISTDIR)
-	@echo "making $(DISTDIR)"
-	mkdir $(DISTDIR)
-	mkdir $(DISTDIR)/doc
-	mkdir $(DISTDIR)/doc/images
-	mkdir $(DISTDIR)/exe
-	@echo "making $(DISTDIR)/src"
-	mkdir $(DISTDIR)/src
-	mkdir $(DISTDIR)/src/javajars
-	mkdir $(DISTDIR)/src/icons
-	mkdir $(DISTDIR)/src/testdata
-	@echo "Copying testdata files from $(TEST_DIR) to $(DISTDIR)/src/testdata..."
-	for i in $(TESTDIR); do \
-      	  mkdir $(DISTDIR)/src/testdata/$$i; \
-      	  cp $(TEST_DIR)/$$i/*.txt $(DISTDIR)/src/testdata/$$i; \
-    	done
-	mkdir $(DISTDIR)/exe/testdata
-	@echo "Copying testdata files from $(TEST_DIR) to $(DISTDIR)/exe/testdata..."
-	for i in $(TESTDIR); do \
-      	  mkdir $(DISTDIR)/exe/testdata/$$i; \
-      	  cp $(TEST_DIR)/$$i/*.txt $(DISTDIR)/exe/testdata/$$i; \
-    	done
-	@echo "Copying common files to $(DISTDIR)..."
-	@for i in $(DIST_COMMON) ; do \
-	  cp $$i $(DISTDIR) ; \
-	done 
-	@echo "Copying sources to $(DISTDIR)/src..."
-	@for i in $(SOURCES) ; do \
-	  cp $$i $(DISTDIR)/src ; \
-	done
-	@echo "Copying icons to $(DISTDIR)/src/icons..."
-	@for i in $(ICONS) ; do \
-	  cp $$i $(DISTDIR)/src/icons ; \
-	done
-	@echo "Copying Java code to $(DISTDIR)/src/javajars...." ; \
-	for i in $(JAVAJAR) ; do \
-	  cp $$i $(DISTDIR)/src/javajars ; \
-	done
-	@echo "Copying Java programs to $(DISTDIR)/exe...." ; \
-	for i in $(JAVAEXE) ; do \
-	  cp $$i $(DISTDIR)/exe ; \
-	done
-	@echo "Copying docs from $(DOC_DIR) to $(DISTDIR)/doc..."
-	@for i in $(DOCS) ; do \
-	  cp $(DOC_DIR)/$$i $(DISTDIR)/doc ; \
-	done
-	@echo "Copying images from $(IMG_DIR) to $(DISTDIR)/doc/images..."
-	@for i in $(IMAGES) ; do \
-	  cp $(IMG_DIR)/$$i $(DISTDIR)/doc/images ; \
-	done
-	@echo "Copying executables to $(DISTDIR)/exe..."
-	@for i in $(W_EXES) ; do \
-	  cp $$i $(DISTDIR)/exe ; \
-	done
-	@for i in $(ASCII_EXT) ; do \
-	  echo "Translating newline characters on *$$i..." ; \
-	  find $(DISTDIR) -name "*$$i" \
-	    -exec sed -i -e 's/$$/\r/g' '{}' ';' ; \
-	done
-
-distclean : clean
-	@echo -n "Removing dists..."
-	@for i in $(DISTDIR) $(DISTDIR).zip $(DISTDIR).exe $(DISTDIR).tar.gz \
-	  phylipw.zip phylipw.exe ; do \
-	  rm -rf $$i ; \
-	done
-	@echo "done."
-	
-
-# vim: noet 

=== removed file 'src/Makefile.osx'
--- src/Makefile.osx	2013-08-07 22:17:03 +0000
+++ src/Makefile.osx	1970-01-01 00:00:00 +0000
@@ -1,678 +0,0 @@
-# Makefile
-#
-# Mac Makefile for PHYLIP 3.695
-
-PACKAGE=phylip
-VERSION=3.695
-
-# We use GNU's version of the make utility. It may be called "gmake" on
-# your system.
-#
-# If you're using a RedHat Linux system with default locations for 
-# gcc libraries, you probably don't need to change anything. You might
-# might change the first noncomment statement below to redefine $(EXEDIR)
-# if you'd like your executables installed in a different location than
-# our default.
-#
-# Users with systems that differ substantially from ours may need to set
-# the following variables: $(CC) $(CFLAGS) $(LIBS) 
-#
-# When uncompressed and extracted, the tar archive phylip-3.6x.tar.gz 
-# produces the following directory structure:
-#
-#   phylip-3.6x/src -- the source code, including this Makefile
-#   phylip-3.6x/exe -- executables, changed by changing $(EXEDIR) value
-#   phylip-3.6x/doc -- html documentation
-#
-#  To use the PHYLIP v3.6 Makefile, type from the phylip-3.6x/src directory:
-#
-#      make install         to compile the whole package and install
-#                           the executables in $(EXEDIR), and then
-#                           remove the object files to save space
-#
-#      make all             to compile the whole package but not install it
-#                           or remove the object files. 
-#
-#      make put             to move the executables into $(EXEDIR)
-#
-#      make clean           to remove all object files and executables from the
-#                           current directory
-#
-#      make dnaml           to compile and link one program, (in this example,
-#                           DnaML) and leave the executable and object files
-#                           in the current directory (where the source code is).
-#                           You will have to move the executable into the
-#                           executables directory (e.g. "mv dnaml ../exe")
-#                           Note that the program name should be lower case.
-# 
-# ----------------------------------------------------------------------------
-#  (Starting here is the section where you may want to change things)
-# ----------------------------------------------------------------------------
-#
-# the following specifies the directory where the executables will be placed
-EXEDIR  = ../exe
-# the following specifies the directory where the testdata will be placed
-TESTDIR  = ../exe/testdata
-#
-# ----------------------------------------------------------------------------
-#
-# The following statements set these variables:
-#
-#    CC     -- the name (and, optionally, location) of your C compiler
-#    CFLAGS -- compiler directives needed to compile most programs
-#    LIBS   -- non-default system libraries needed to compile most programs
-#
-# We've provided a set of possible values for each variable.
-#
-# The value used is the one without a "#" at the beginning of the line.
-#
-# To try an alternate value, make sure the one you want has no "#"
-# as its first character and that all other possibilities have "#" for
-# their first character.
-#
-# Advanced users may need to further edit one of the alternatives in
-# order to correctly compile on their system.
-#
-# ----------------------------------------------------------------------------
-#
-# The next two assignments are the invocations of the compiler
-#
-# This one specifies the "cc" C compiler
-#CC        = cc
-#
-#  To use GCC instead:
-CC        = gcc
-#
-# ----------------------------------------------------------------------------
-#
-# This is the CFLAGS statement. It specifies compiler behavior.
-#
-# Here are some possible CFLAGS statements:
-#
-#
-#A minimal one which tells Phylip that is is running on a modern Mac
-#CFLAGS = -DMACOS10
-#
-# A basic one for debugging
-CFLAGS  = -ggdb -DMACOS10
-#
-# An optimized one for gcc
-#CFLAGS  = -O3 -DMACOS10 -fomit-frame-pointer
-#
-# For some serious debugging using Gnu gcc
-#
-#CFLAGS=-g -DMACOS10 -Wall -Wmain -Wmissing-prototypes -Wreturn-type -Wstrict-prototypes  -Wunused -Werror -Wredundant-decls -Waggregate-return -Wcast-align -Wcomment
-#
-# For doing code coverage with gcov
-#
-#CFLAGS	=	-ggdb -DMACOS10 -fprofile-arcs -ftest-coverage
-#CFLAGS	=	-pg -DMACOS10
-#
-# For Digital Alpha systems with Compaq Tru64 Unix
-# (however, be aware that this may cause floating-point problems in programs
-#  like Dnaml owing to not using IEEE floating point standards).
-#CFLAGS = -fast -DMACOS10
-# ----------------------------------------------------------------------------
-#
-# Most of the programs need only the math libraries, specified like this;
-#
-LIBS    = -lm
-#
-#
-# ----------------------------------------------------------------------------
-#  (After this point there should not be any reason to change anything)
-# ----------------------------------------------------------------------------
-#
-#
-# the list of programs
-# draw programs are listed last since they are the most likely to cause
-# compilation or linking problems
-
-PROGS   =		clique \
-				consense \
-				contml \
-				contrast \
-				dnacomp \
-				dnadist \
-				dnainvar \
-				dnaml \
-				dnamlk \
-				dnamove \
-				dnapars \
-				dnapenny \
-				dolmove \
-				dollop \
-				dolpenny \
-				factor \
-				fitch \
-				gendist \
-				kitsch \
-				mix \
-				move \
-				neighbor \
-				pars \
-				penny \
-				proml \
-				promlk \
-				protdist \
-				protpars \
-				restdist \
-				restml \
-				retree \
-				seqboot \
-				treedist \
-        		drawgram \
-				drawtree 
-							
-DYLIBS  =       libdrawgram.dylib \
-				libdrawtree.dylib
-
-JARS    =       javajars/DrawGram.jar \
-                javajars/DrawTree.jar
-
-APPS    =          clique.app consense.app contml.app contrast.app dnacomp.app \
-                   dnadist.app dnainvar.app dnaml.app dnamlk.app dnamove.app \
-                   dnapars.app dnapenny.app dollop.app dolmove.app dolpenny.app \
-                   drawgram.app drawtree.app factor.app fitch.app gendist.app \
-                   kitsch.app mix.app move.app neighbor.app pars.app penny.app \
-                   proml.app promlk.app protdist.app protpars.app restdist.app \
-                   restml.app retree.app seqboot.app treedist.app 
-#
-# general commands
-#
-
-#  The first target it executed if you just type "make".  It tells you how to
-#  use the Makefile.
-#
-help:
-	@echo ""
-	@echo " To use the PHYLIP v$(VERSION) Makefile, type"
-	@echo "     make install       to compile the whole package and install"
-	@echo "                          the executables in $(EXEDIR), and then"
-	@echo "                          remove the object files to save space"
-	@echo "     make all           to compile the whole package but not install it"
-	@echo "                          or remove the object files"
-	@echo "     make put           to move the executables into $(EXEDIR)"
-	@echo "     make clean         to remove all object files and executables from the"
-	@echo "                          current directory"
-	@echo "     make dnaml         to compile and link one program, (in this example,"
-	@echo "                          Dnaml) and leave the executable and object files"
-	@echo "                          in the current directory (where the source code is)."
-	@echo "                          You will have to move the executable into the"
-	@echo "                          executables directory (e.g. \"mv dnaml $(EXEDIR)\")"
-	@echo "                          Note that the program name should be lower case."
-	@echo " "
-
-introduce:
-	@echo "Building PHYLIP version $(VERSION)"
-
-all:        introduce $(PROGS) $(DYLIBS) 
-	@echo "Finished compiling."
-	@echo ""
-
-# For making clickable executables.
-apps:   $(APPS) $(DYLIBS)
-
-install:    pre-clean apps  put clean
-	@echo "Done."
-	@echo ""
-
-put:
-	@echo "Installing PHYLIP v3.6 binaries in $(EXEDIR)"
-	@mkdir -p $(EXEDIR)
-	@for i in $(APPS) ; do \
-         rm -rf "$(EXEDIR)/$$i" ; \
-         done
-	@mv $(APPS) '$(EXEDIR)'
-	@echo "Installing dynamic libraries in $(EXEDIR)"
-	@cp $(DYLIBS) $(EXEDIR)
-	@echo "Installing jar files in $(EXEDIR)"
-	@cp $(JARS) $(EXEDIR)
-	@echo "Installing font files in $(EXEDIR)"
-	@cp font* $(EXEDIR)
-	@echo "Copying testdata to $(EXEDIR)/testdata"
-	mkdir $(EXEDIR)/testdata
-	for i in $(TESTDIR); do \
-      mkdir $(EXEDIR)/testdata/$$i; \
-      cp testdata/$$i/*.txt $(EXEDIR)/testdata/$$i; \
-    done
-	@echo "Finished installation."
-	@echo ""
-
-pre-clean:
-	@echo "Removing preexisting executables"
-	@for i in $(APPS) ; do \
-      rm -rf "$(EXEDIR)/$$i" ; \
-    done
-	@echo "Removing preexisting testdata"
-	@rm -rf $(EXEDIR)/testdata
-	@echo "Ready for new executables"
-	@echo ""
-
-clean:
-	@echo "Removing object files to save space"
-	@rm -f *.o
-	@rm -f $(DYLIBS)
-	@echo "Finished removing object files.  Now will remove"
-	@echo "executable files from the current directory, but not from the"
-	@echo "executables directory.  (If some are not here, the makefile"
-	@echo "will terminate with an error message but this is not a problem)"
-	@echo ""
-	@echo "Removing executables from this directory"
-	@rm -f $(PROGS)
-	@rm -rf $(APPS)
-	@echo "Finished cleanup."
-	@echo ""
-
-#
-# compile object files shared between programs
-# (make's implicit rule for %.o will take care of these)
-#
-
-phylip.o:     phylip.h
-seq.o:        phylip.h seq.h
-disc.o:       phylip.h disc.h
-discrete.o:   phylip.h discrete.h
-dollo.o:      phylip.h dollo.h
-wagner.o:     phylip.h wagner.h
-dist.o:       phylip.h dist.h
-cont.o:       phylip.h cont.h
-mlclock.o:    phylip.h mlclock.h
-moves.o:      phylip.h moves.h
-printree.o:   phylip.h printree.h
-
-#
-# compile the individual programs
-#
-
-clique.o:       clique.c disc.h phylip.h
-
-clique:         clique.o disc.o phylip.o
-	$(CC) $(CFLAGS) clique.o disc.o phylip.o $(LIBS) -o clique
-
-cons.o:         cons.c cons.h phylip.h 
-
-consense.o:     consense.c cons.h phylip.h
-
-consense:       consense.o phylip.o cons.o
-	$(CC) $(CFLAGS) consense.o phylip.o cons.o $(LIBS) -o consense
-
-contml.o:       contml.c cont.h phylip.h
-
-contml:       contml.o cont.o phylip.o
-	$(CC) $(CFLAGS) contml.o cont.o phylip.o $(LIBS) -o contml
-
-contrast.o:       contrast.c cont.h phylip.h
-
-contrast:       contrast.o cont.o phylip.o
-	$(CC) $(CFLAGS) contrast.o cont.o phylip.o $(LIBS) -o contrast
-
-dnacomp.o:      dnacomp.c seq.h phylip.h
-
-dnacomp:      dnacomp.o seq.o phylip.o
-	$(CC) $(CFLAGS) dnacomp.o seq.o phylip.o $(LIBS) -o dnacomp
-
-dnadist.o:      dnadist.c seq.h phylip.h
-
-dnadist:      dnadist.o seq.o phylip.o
-	$(CC) $(CFLAGS) dnadist.o seq.o phylip.o $(LIBS) -o dnadist
-
-dnainvar.o:      dnainvar.c seq.h phylip.h
-
-dnainvar:      dnainvar.o seq.o phylip.o
-	$(CC) $(CFLAGS) dnainvar.o seq.o phylip.o $(LIBS) -o dnainvar
-
-dnaml.o:      dnaml.c seq.h phylip.h
-
-dnaml:      dnaml.o seq.o phylip.o
-	$(CC) $(CFLAGS) dnaml.o seq.o phylip.o $(LIBS) -o dnaml
-
-dnamlk.o:      dnamlk.c seq.h phylip.h mlclock.h printree.h
-
-dnamlk:      dnamlk.o seq.o phylip.o mlclock.o printree.o
-	$(CC) $(CFLAGS) dnamlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o dnamlk
-
-dnamove.o:      dnamove.c seq.h moves.h phylip.h
-
-dnamove:      dnamove.o seq.o moves.o phylip.o
-	$(CC) $(CFLAGS) dnamove.o seq.o moves.o phylip.o $(LIBS) -o dnamove
-
-dnapenny.o:      dnapenny.c seq.h phylip.h
-
-dnapenny:      dnapenny.o seq.o phylip.o
-	$(CC) $(CFLAGS) dnapenny.o seq.o phylip.o $(LIBS) -o dnapenny
-
-dnapars.o:      dnapars.c seq.h phylip.h
-
-dnapars:      dnapars.o seq.o phylip.o
-	$(CC) $(CFLAGS) dnapars.o seq.o phylip.o $(LIBS) -o dnapars
-
-dolmove.o:       dolmove.c disc.h moves.h dollo.h phylip.h
-
-dolmove:       dolmove.o disc.o moves.o dollo.o phylip.o
-	$(CC) $(CFLAGS) dolmove.o disc.o moves.o dollo.o phylip.o $(LIBS) -o dolmove
-
-dollop.o:       dollop.c disc.h dollo.h phylip.h
-
-dollop:       dollop.o disc.o dollo.o phylip.o
-	$(CC) $(CFLAGS) dollop.o disc.o dollo.o phylip.o $(LIBS) -o dollop
-
-dolpenny.o:       dolpenny.c disc.h dollo.h phylip.h
-
-dolpenny:       dolpenny.o disc.o dollo.o phylip.o
-	$(CC) $(CFLAGS) dolpenny.o disc.o dollo.o phylip.o $(LIBS) -o dolpenny
-
-draw.o:   draw.c draw.h phylip.h 
-	$(CC) $(CFLAGS) -c draw.c
-
-draw2.o:   draw2.c draw.h phylip.h 
-	$(CC) $(CFLAGS) -c draw2.c
-
-drawgram.o:     drawgram.c draw.h phylip.h
-	$(CC) $(CFLAGS) -c drawgram.c
-
-drawgram:     drawgram.o draw.o draw2.o phylip.o
-	$(CC) $(CFLAGS) draw.o draw2.o drawgram.o phylip.o $(CLIBS) -o drawgram
-	
-# needed by java	
-libdrawgram.dylib:     drawgram.o draw.o draw2.o phylip.o
-	$(CC) $(CFLAGS)  -shared drawgram.o draw.o draw2.o phylip.o $(CLIBS) -o libdrawgram.dylib
-
-drawtree.o:     drawtree.c draw.h phylip.h
-	$(CC) $(CFLAGS) -c drawtree.c
-
-drawtree:     drawtree.o draw.o draw2.o phylip.o
-	$(CC) $(CFLAGS) draw.o draw2.o drawtree.o phylip.o $(CLIBS) -o drawtree
-
-# needed by java	
-libdrawtree.dylib:     drawtree.o draw.o draw2.o phylip.o
-	$(CC) $(CFLAGS)  -shared drawtree.o draw.o draw2.o phylip.o $(CLIBS) -o libdrawtree.dylib
-
-factor.o:       factor.c phylip.h
-
-factor:       factor.o phylip.o
-	$(CC) $(CFLAGS) factor.o phylip.o $(LIBS) -o factor
-
-fitch.o:        fitch.c dist.h phylip.h
-
-fitch:        fitch.o dist.o phylip.o
-	$(CC) $(CFLAGS) fitch.o dist.o phylip.o $(LIBS) -o fitch
-
-gendist.o:      gendist.c phylip.h
-
-gendist:      gendist.o phylip.o
-	$(CC) $(CFLAGS) gendist.o phylip.o $(LIBS) -o gendist
-
-kitsch.o:        kitsch.c dist.h phylip.h
-
-kitsch:        kitsch.o dist.o phylip.o
-	$(CC) $(CFLAGS) kitsch.o dist.o phylip.o $(LIBS) -o kitsch
-
-mix.o:        mix.c disc.h wagner.h phylip.h
-
-mix:        mix.o disc.o wagner.o phylip.o
-	$(CC) $(CFLAGS) mix.o disc.o wagner.o phylip.o $(LIBS) -o mix
-
-move.o:        move.c disc.h moves.h wagner.h phylip.h
-
-move:        move.o disc.o moves.o wagner.o phylip.o
-	$(CC) $(CFLAGS) move.o disc.o moves.o wagner.o phylip.o $(LIBS) -o move
-
-neighbor.o:        neighbor.c dist.h phylip.h
-
-neighbor:        neighbor.o dist.o phylip.o
-	$(CC) $(CFLAGS) neighbor.o dist.o phylip.o $(LIBS) -o neighbor
-
-pars.o:   pars.c discrete.h phylip.h
-
-pars: pars.o discrete.o phylip.o
-	$(CC) $(CFLAGS) pars.o discrete.o phylip.o $(LIBS) -o pars
-
-penny.o:  penny.c disc.h wagner.h phylip.h
-
-penny:  penny.o disc.o wagner.o phylip.o
-	$(CC) $(CFLAGS) penny.o disc.o wagner.o  phylip.o $(LIBS) -o penny
-
-proml.o:      proml.c seq.h phylip.h
-
-proml:      proml.o seq.o phylip.o
-	$(CC) $(CFLAGS) proml.o seq.o phylip.o $(LIBS) -o proml
-
-promlk.o:      promlk.c seq.h phylip.h mlclock.h printree.h
-
-promlk:      promlk.o seq.o phylip.o mlclock.o printree.o
-	$(CC) $(CFLAGS) promlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o promlk
-
-protdist.o:      protdist.c seq.h phylip.h
-
-protdist:      protdist.o seq.o phylip.o
-	$(CC) $(CFLAGS) protdist.o seq.o phylip.o $(LIBS) -o protdist
-
-protpars.o: protpars.c seq.h phylip.h
-
-protpars: protpars.o seq.o phylip.o
-	$(CC) $(CFLAGS) protpars.o seq.o phylip.o $(LIBS) -o protpars
-
-restdist.o: restdist.c seq.h phylip.h
-
-restdist: restdist.o seq.o phylip.o
-	$(CC) $(CFLAGS) restdist.o seq.o phylip.o $(LIBS) -o restdist
-
-restml.o: restml.c seq.h phylip.h
-
-restml: restml.o seq.o phylip.o
-	$(CC) $(CFLAGS) restml.o seq.o phylip.o $(LIBS) -o restml
-
-retree.o:       retree.c moves.h phylip.h
-
-retree:       retree.o moves.o phylip.o
-	$(CC) $(CFLAGS) retree.o moves.o phylip.o $(LIBS) -o retree
-
-seqboot.o:      seqboot.c phylip.h
-
-seqboot:      seqboot.o seq.o phylip.o
-	$(CC) $(CFLAGS) seqboot.o seq.o phylip.o $(LIBS) -o seqboot
-
-treedist.o:     treedist.c cons.h phylip.h
-
-treedist:     treedist.o phylip.o cons.o
-	$(CC) $(CFLAGS) treedist.o cons.o phylip.o $(LIBS) -o treedist
-
-#
-# This is where the clickable executables are made for Mac OSX
-#
-%.app: % mac/Info.plist.in mac/command.in mac/%.icns 
-	@rm -rf $@
-	/Developer/Tools/Rez -d __DARWIN__ -t APPL Carbon.r -o $<
-	/Developer/Tools/SetFile -a C $<
-	-mkdir -p $@/Contents/MacOS
-	-mkdir -p $@/Contents/Resources
-	sed -e "s/IDENTIFIER/$</" \
-	-e "s/COMMAND/$<.command/" \
-	-e "s/EXECUTABLE/$</" \
-	-e "s/ICONNAME/$</" \
-	-e "s/VERSION/$(VERSION)/" \
-	mac/Info.plist.in > $@/Contents/Info.plist
-	sed -e "s/EXECUTABLE/$</" \
-	mac/command.in > $@/Contents/MacOS/$<.command
-	chmod ug+x $@/Contents/MacOS/$<.command
-	echo -n "APPL????" >$@/Contents/PkgInfo
-	cp $< $@/Contents/MacOS/$<
-	cp -f mac/$<.icns $@/Contents/Resources/$<.icns
-
-# Location of the lsregister command to force re-registration with LaunchServices
-LSREGISTER=/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister
-
-%.install:	%.app
-	@rm -rf '$(EXEDIR)/$<'
-	@mv $< '$(EXEDIR)'
-	
-# ----------------------------------------------------------------------------
-#  The following section is used to build a PHYLIP distribution. All sources
-#  and other files except the documentation files must be placed in the
-#  current directory.  The HTML documentation files must be in folder "doc"
-#  within this, the Mac icons in folder "mac", and the Windows icons and
-#  resource files must be in folder "icons"
-#
-#  Usage:
-#  	make distdir	- Build the distribution dir phylip-<vers>/
-#  	make dist	- Make a tarred and gzipped phylip-<vers>.tar.gz
-# ----------------------------------------------------------------------------
-
-DIST_COMMON = phylip.html 
-
-DOCS= doc/clique.html doc/consense.html doc/contchar.html doc/contml.html \
-      doc/contrast.html doc/discrete.html doc/distance.html doc/dnacomp.html \
-      doc/dnadist.html doc/dnainvar.html doc/dnaml.html doc/dnamlk.html \
-      doc/dnamove.html doc/dnapars.html doc/dnapenny.html doc/dollop.html \
-      doc/dolmove.html doc/dolpenny.html doc/drawgram.html doc/draw.html \
-      doc/drawtree.html doc/factor.html doc/fitch.html doc/gendist.html \
-      doc/kitsch.html doc/main.html doc/mix.html doc/move.html \
-      doc/neighbor.html doc/pars.html doc/penny.html doc/proml.html \
-      doc/promlk.html doc/protdist.html doc/protpars.html doc/restdist.html \
-      doc/restml.html doc/retree.html doc/seqboot.html doc/sequence.html \
-      doc/treedist.html doc/phylip.gif
-      
-IMAGES= doc/images/DrawGramCat.png doc/images/DrawGramControls.png \
-     doc/images/DrawTreeCat.png doc/images/DrawTreeControls.png \
-     doc/images/InputTree.png
-
-SOURCES= COPYRIGHT Makefile.cyg Makefile.osx Makefile.unx linkmac \
-     clique.c cons.c consense.c cons.h cont.c \
-     cont.h contml.c contrast.c disc.c disc.h discrete.c discrete.h dist.c \
-	 dist.h dnacomp.c dnadist.c dnainvar.c dnaml.c dnamlk.c dnamove.c \
-	 dnapars.c dnapenny.c dollo.c dollo.h dollop.c dolmove.c dolpenny.c \
-	 draw2.c draw.c drawgram.c draw.h drawtree.c \
-	 factor.c fitch.c gendist.c \
-	 interface.c interface.h io.h kitsch.c macface.c macface.h mix.c move.c \
-	 moves.c moves.h neighbor.c newmove.c pars.c penny.c \
-	 phylip.c phylip.h proml.c promlk.c protdist.c protpars.c restdist.c \
-	 restml.c retree.c seqboot.c seq.c seq.h treedist.c wagner.c wagner.h \
-	 mlclock.c mlclock.h printree.c printree.h
-
-MAC= \
-		Info.plist.in boot.icns clique.icns command.in consense.icns \
-	contml.icns contrast.icns disc.icns dist.icns dna.icns dnacomp.icns \
-	dnadist.icns dnainvar.icns dnaml.icns dnamlk.icns dnamove.icns \
-	dnapars.icns dnapenny.icns dollo.icns dollop.icns dolmove.icns \
-	dolpenny.icns drawgram.icns drawtree.icns factor.icns fitch.icns \
-	gendist.icns kitsch.icns mac.sit mix.icns move.icns neighbor.icns \
-	pars.icns penny.icns proml.icns promlk.icns protdist.icns protein.icns \
-	protpars.icns restdist.icns restml.icns restrict.icns retree.icns \
-	seqboot.icns treedist.icns
-
-ICONS= 		boot.ico clique.ico clique.rc clique.rcb consense.ico \
-		consense.rc consense.rcb contml.ico contml.rc contml.rcb \
-		contrast.ico contrast.rc contrast.rcb disc.ico dist.ico dna.ico \
-		dnacomp.rc dnacomp.rcb dnadist.rc dnadist.rcb dnainvar.rc \
-		dnainvar.rcb dnaml.rc dnaml.rcb dnamlk.rc dnamlk.rcb dnamove.rc \
-		dnamove.rcb dnapars.rc dnapars.rcb dnapenny.rc dnapenny.rcb \
-		dollo.ico dollop.rc dollop.rcb dolmove.rc dolmove.rcb \
-		dolpenny.rc dolpenny.rcb drawgram.ico drawgram.rc drawgram.rcb \
-		drawtree.ico drawtree.rc drawtree.rcb factor.rc factor.rcb \
-		fitch.rc fitch.rcb gendist.ico gendist.rc gendist.rcb kitsch.rc \
-		kitsch.rcb mix.rc mix.rcb move.rc move.rcb neighbor.rc \
-		neighbor.rcb pars.rc pars.rcb penny.rc penny.rcb proml.rc \
-		proml.rcb promlk.rc promlk.rcb protdist.rc protdist.rcb \
-		protein.ico protpars.rc protpars.rcb restdist.rc restdist.rcb \
-		restml.rc restml.rcb restrict.ico retree.ico retree.rc \
-		retree.rcb seqboot.rc seqboot.rcb treedist.ico treedist.rc \
-		treedist.rcb
-
-FONTS= font1 font2 font3 font4 font5 font6
-
-TESTDIR=   clique consense contml contrast dnacomp \
-      dnadist dnainvar dnaml dnamlk dnamove dnapars dnapenny dollop \
-      dolmove dolpenny drawgram drawtree factor fitch gendist \
-      kitsch mix move neighbor pars penny proml promlk \
-      protdist protpars restdist restml retree seqboot  treedist
-      
-JARAJAR=    javajars/DrawGram.jar javajars/DrawTree.jar \
-        javajars/DrawGramJava.bat javajars/DrawTreeJava.bat \
-        javajars/DrawGramJava.exe javajars/DrawTreeJava.exe \
-        javajars/DrawGramJava.unx javajars/DrawTreeJava.unx
-        
-      
-DISTDIR=$(PACKAGE)-$(VERSION)-osx
-dist_SRCDIR=$(DISTDIR)/src
-dist_DOCDIR=$(DISTDIR)/doc
-dist_IMGDIR=$(DISTDIR)/doc/images
-dist_EXEDIR=$(DISTDIR)/exe
-dist_JAVADIR=$(DISTDIR)/src/javajars
-MACICONDIR=src/mac
-
-SHELL=bash
-
-# We can use this target to create a tarred and gzipped distribution of PHYLIP
-dist: distdir
-	-chmod -R a+r $(DISTDIR)
-	tar chozf $(DISTDIR).tar.gz $(DISTDIR)
-	-rm -rf $(DISTDIR)
-
-# This target creates the distribution directory which buildDmg.sh uses to build install "disk"
-distdir: $(DIST_COMMON) $(DOCS) $(SOURCES)
-	-rm -rf $(DISTDIR)
-	mkdir $(DISTDIR) && \
-	mkdir $(dist_EXEDIR) && \
-	mkdir $(dist_DOCDIR) && \
-	mkdir $(dist_IMGDIR) && \
-	mkdir $(dist_SRCDIR) && \
-	mkdir $(dist_JAVADIR)
-	mkdir $(dist_SRCDIR)/mac
-	mkdir $(dist_SRCDIR)/icons
-	mkdir $(dist_SRCDIR)/testdata