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251. By Jon Hill on 2014-09-18

random ci so I can merge into a properly names branch

250. By Jon Hill on 2014-06-18

Update to changelog for release 12

249. By Jon Hill on 2014-06-16

Fix bug 1246895 which is a minor irritation when subbing taxa - the outgroups weren't dealt with and the taxa listed in the XML got mangled when subbing in a polytomy. Outgroups are dealt with and the taxa blocks are copied and replaced correctly with polytomies.

248. By Jon Hill on 2014-06-16

Moving output of permute_trees to directories rather than different files. For large datasets this makes for cleaner output and is easier to script (as the filename is consistent across all outputs). The GUI and CLI both have the same output structure.

247. By Jon Hill on 2014-06-16

Limit weights in TNT to be 3 decimal places only. Otherwise TNT will complain

246. By Jon Hill on 2014-06-16

Minor fix to previous bug fix, hooking up of GUI and documenting options in manual

245. By Jaime Tovar on 2014-06-10

Comment for software inside software

244. By Jon Hill on 2014-06-09

Adding option to accept generic matches as matches when using existing_only option when subbing taxa. Also a bit of refactoring to prevent code duplication

243. By Jon Hill on 2014-06-09

Minor big fix to subbing existing taxa. Don't delete them if none of the incoming ones are not in the dataset. Just retain them

242. By Jaime Tovar on 2014-06-03

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