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Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 10 16:24:10 2010 UTC (9 years, 1 month ago) by fangfang
Branch: MAIN
CVS Tags: rast_rel_2010_1206
Changes since 1.34: +1 -3 lines
Diff to previous 1.34
use SeedAware::run_gathering_output to handle muscle version information

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 29 21:19:03 2010 UTC (9 years, 2 months ago) by fangfang
Branch: MAIN
Changes since 1.33: +8 -1 lines
Diff to previous 1.33
Modify 'version' option for align_with_mafft

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Sep 18 16:26:24 2010 UTC (9 years, 2 months ago) by fangfang
Branch: MAIN
CVS Tags: rast_rel_2010_0928
Changes since 1.32: +189 -0 lines
Diff to previous 1.32
Added align_with_mafft

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 16 23:52:37 2010 UTC (9 years, 2 months ago) by golsen
Branch: MAIN
Changes since 1.31: +30 -25 lines
Diff to previous 1.31
Fix the trim code.
Numerous small changes, including better clean-up of temp files.

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 8 21:04:19 2010 UTC (9 years, 3 months ago) by golsen
Branch: MAIN
Changes since 1.30: +146 -21 lines
Diff to previous 1.30
Work around a clustalw bug in profile alignment at inserts columns of
gaps into an alignment.
Add a clustal_profile_alignment() function.

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Aug 29 22:13:28 2010 UTC (9 years, 3 months ago) by golsen
Branch: MAIN
Changes since 1.29: +240 -98 lines
Diff to previous 1.29
Much code clean-up and consolidation.

New version of add to alignment that does much better gap placement.

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 21 17:21:11 2010 UTC (9 years, 3 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2010_0827
Changes since 1.28: +173 -197 lines
Diff to previous 1.28
Many changes and improvements.  Fixed major add_to_alignment_v2 bug.
Now SeedAware.

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 18 20:12:30 2009 UTC (9 years, 11 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2010_0118, rast_rel_2010_0526
Changes since 1.27: +1 -0 lines
Diff to previous 1.27
mark as SAS component

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Sep 6 22:38:32 2009 UTC (10 years, 3 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2009_0925
Changes since 1.26: +60 -10 lines
Diff to previous 1.26
Add and/or update routines to support bootstrapping and bootstrap consensus
trees.
Fix some undefined values revealed by -w flag.

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 30 21:36:42 2009 UTC (10 years, 5 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2009_07_09
Changes since 1.25: +15 -19 lines
Diff to previous 1.25
Changes mostly in add_to_alignment.

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 26 00:06:26 2009 UTC (10 years, 5 months ago) by golsen
Branch: MAIN
Changes since 1.24: +1 -1 lines
Diff to previous 1.24
New super duper ala Peter T. Hooper paralog resolution interface.

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 23 23:27:09 2009 UTC (10 years, 5 months ago) by golsen
Branch: MAIN
Changes since 1.23: +215 -78 lines
Diff to previous 1.23
Add options to muscle, and set clustalw up for the same (though that is
not done yet).

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 22 19:39:43 2009 UTC (10 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.22: +1 -1 lines
Diff to previous 1.22
fix mispelling

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 22 19:35:59 2009 UTC (10 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.21: +31 -0 lines
Diff to previous 1.21
added stuff

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 22 18:41:05 2009 UTC (10 years, 5 months ago) by golsen
Branch: MAIN
Changes since 1.20: +25 -9 lines
Diff to previous 1.20
Fix trimming in add_to_alignment_v2.

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 22 18:24:13 2009 UTC (10 years, 5 months ago) by golsen
Branch: MAIN
Changes since 1.19: +311 -78 lines
Diff to previous 1.19
Add function add_to_alignment_v2().

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 13 21:25:43 2009 UTC (10 years, 8 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2009_05_18
Changes since 1.18: +15 -11 lines
Diff to previous 1.18
Slight clean-up of code.

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 29 20:24:13 2009 UTC (10 years, 10 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2009_02_05, rast_rel_2009_03_26
Changes since 1.17: +1 -1 lines
Diff to previous 1.17
additions to support partitioning of sims

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 30 04:54:38 2008 UTC (11 years, 1 month ago) by golsen
Branch: MAIN
CVS Tags: mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2, rast_rel_2008_11_24, rast_rel_2008_12_18
Changes since 1.16: +3 -3 lines
Diff to previous 1.16
Fixed a bug introduced into align_with_clustal() that caused it to return
[ id, seq ] pairs, rather than [ id, definition, seq ] in certain
circumstances.

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 25 18:14:45 2008 UTC (11 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.15: +32 -7 lines
Diff to previous 1.15
updates from Gary

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 14 17:21:53 2008 UTC (11 years, 4 months ago) by golsen
Branch: MAIN
CVS Tags: mgrast_rel_2008_0625, mgrast_rel_2008_0806, mgrast_rel_2008_0917, mgrast_rel_2008_0919, mgrast_rel_2008_0923, mgrast_rel_2008_0924, rast_2008_0924, rast_rel_2008_09_29, rast_rel_2008_09_30, rast_rel_2008_10_09, rast_rel_2008_10_29, rast_release_2008_09_29
Changes since 1.14: +15 -12 lines
Diff to previous 1.14
Fix FIG dependencies so that it is FIG-aware, but not FIG-dependent.

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 12 20:12:56 2007 UTC (12 years, 7 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2008_04_23, rast_rel_2008_06_16, rast_rel_2008_06_18, rast_rel_2008_07_21, rast_rel_2008_08_07
Changes since 1.13: +5 -2 lines
Diff to previous 1.13
add utilities for computing alignments

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 10 03:49:06 2007 UTC (12 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.12: +1 -1 lines
Diff to previous 1.12
Fixed some compiler warnings.

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 9 21:00:24 2007 UTC (12 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.11: +3 -1 lines
Diff to previous 1.11
Major change in the alignment and tree portions of fid_checked.
Nicer alignment display.
Clean-up of tree display and underlying libraries.
Caching of the alignment and tree so that display paramters and/or
assignments can be updated without recomputing the alignment and tree.

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 9 00:39:43 2007 UTC (12 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.10: +87 -12 lines
Diff to previous 1.10
Add an align_with_clustal function to the module.

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 18 17:25:19 2007 UTC (12 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.9: +3 -3 lines
Diff to previous 1.9
add filter_figfams.pl

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 24 01:33:07 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.8: +31 -2 lines
Diff to previous 1.8
fix to retrimming alignments

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 21 17:05:18 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.7: +3 -0 lines
Diff to previous 1.7
current versions of FigFam.pm

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Feb 11 22:37:11 2007 UTC (12 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +1 -1 lines
Diff to previous 1.6
add PHOB.pm to support some phylogeny stuff

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 20 20:43:54 2006 UTC (12 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +9 -5 lines
Diff to previous 1.5
bug fixes in adding to an alignment -- trimming was lost

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 19 18:35:08 2006 UTC (12 years, 11 months ago) by golsen
Branch: MAIN
Changes since 1.4: +15 -9 lines
Diff to previous 1.4
Add more flexible interface for files: handle, name or default.

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 15 00:09:52 2006 UTC (13 years ago) by overbeek
Branch: MAIN
Changes since 1.3: +60 -1 lines
Diff to previous 1.3
add ability to insert sequences into a tree

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 29 19:28:11 2005 UTC (13 years, 11 months ago) by golsen
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
Changes since 1.2: +16 -8 lines
Diff to previous 1.2
Make attempt to add a duplicate id nonfatal.  Having the program die
in the middle of a large number of adds is annoying.
Increase flexibility on return data type (array or reference to array)
in the function library.
Make the calls by reference in the program.

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 5 19:06:30 2005 UTC (14 years ago) by olson
Branch: MAIN
Changes since 1.1: +17 -0 lines
Diff to previous 1.1
Added license words.

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 7 02:16:00 2005 UTC (14 years, 6 months ago) by golsen
Branch: MAIN
CVS Tags: Root-bobdev_news, caBIG-00-00-00, caBIG-dataload-0, merge-bobdev_news-1, merge-bobdev_news-2, merge-bodev_news-3, merge-trunktag-bobdev_news-1, merge-trunktag-bobdev_news-2, merge-trunktag-bodev_news-3
Branch point for: Branch-bobdev_news
Add a module with some routines for adding sequences to alignments.

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