Timeline
04/29/10:
- 21:54 Changeset [578] by
- addition of new protein models
- 00:35 Changeset [577] by
- added paml2dawg R program to transform paml matrices to dawg matrices
04/28/10:
- 18:24 Changeset [576] by
- residue model
- 17:51 Changeset [575] by
- typo
- 17:46 Changeset [574] by
- gcc doesn't like char in right_align, use string (see previous commit)
- 17:45 Changeset [573] by
- framework for aa models
04/24/10:
- 01:01 Changeset [572] by
- append and split options implemented
04/23/10:
- 00:06 Changeset [571] by
- new command line options compiling fix on windows
04/21/10:
- 18:19 Changeset [570] by
- code comments
- 18:18 Changeset [569] by
- use uniform scale
- 17:25 Changeset [568] by
- typos; bugfixes; wagstar
- 14:24 Changeset [567] by
- amion acid model; woot
04/20/10:
- 18:47 Changeset [566] by
- star wag model
- 18:36 Changeset [565] by
- aagtr model
- 18:20 Changeset [564] by
- simplify substitution headers
- 17:39 Changeset [563] by
- gapoverlap of root controls entire section
- 17:05 Changeset [562] by
- cache some alignment information
- 14:49 Changeset [561] by
- check for spirit 2.2
- 00:16 Changeset [560] by
- output formats
04/19/10:
- 22:53 Changeset [559] by
- obey arg.output
- 02:11 Changeset [558] by
- output work; sequence header
- 00:22 Changeset [557] by
- bug fix
04/18/10:
- 23:25 Changeset [556] by
- removed is_singular warning
- 22:33 Changeset [555] by
- compiling on windows and with boost 1.42
- 20:44 Changeset [554] by
- don't need to look for bison and flex
04/16/10:
- 18:47 Changeset [553] by
- output class
- 18:27 Changeset [552] by
- begin creating output class
- 18:26 Changeset [551] by
- begin creating output class
- 17:10 Changeset [550] by
- bug fix related to deleted sites
- 16:46 Changeset [549] by
- do not compile old files
- 15:47 Changeset [548] by
- tree scaling supported
- 15:10 Changeset [547] by
- limit alignment to output sequences
04/15/10:
- 17:28 Changeset [546] by
- thoughts on using boost::regex
- 16:47 Changeset [545] by
- use boost::sub_range
- 15:57 Changeset [544] by
- input file aliases
- 15:23 Changeset [543] by
- option to remove empty gaps
- 14:47 Changeset [542] by
- only one root per segment
04/14/10:
- 18:55 Changeset [541] by
- algo for removing empty columns
- 17:09 Changeset [540] by
- LowerCase? and MarkIns? segment options
- 15:28 Changeset [539] by
- new residue exchange model
04/13/10:
- 18:43 Changeset [538] by
- replicates; new rex interfance
04/09/10:
- 14:29 Changeset [537] by
- autonaming of sections using -? works
04/08/10:
- 18:45 Changeset [536] by
- start work on makeing -? an autonamed section
- 18:36 Changeset [535] by
- don't allow section headers to be empty (Reversion)
- 18:23 Changeset [534] by
- replaced several usages of maps with vectors and precached indices
- 14:30 Changeset [533] by
- changed support for internal and hidden labels
04/07/10:
- 18:53 Changeset [532] by
- work on indexing node labels
- 18:33 Changeset [531] by
- simplifed pile whitespace
- 18:29 Changeset [530] by
- comments in pile format should eend at eoi as well
- 18:17 Changeset [529] by
- branch_color now updated properly
- 17:48 Changeset [528] by
- whitespace cleanup
- 17:47 Changeset [527] by
- code reform
- 17:08 Changeset [526] by
- patched together a working aligner
04/05/10:
- 18:31 Changeset [525] by
- alignment type
- 17:56 Changeset [524] by
- more bug fixes; Sim.Seed supports arrays
- 17:22 Changeset [523] by
- compiling issues; assert bug; NULL and empty string same as - for cin …
04/01/10:
- 18:21 Changeset [522] by
- continued work on building new interface
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