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Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 14 17:21:53 2008 UTC (11 years, 6 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, 9 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, 10 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, 10 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, 10 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, 11 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 (13 years 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 (13 years 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 (13 years 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 (13 years, 2 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 (13 years, 2 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, 2 months 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 (14 years, 1 month 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, 2 months 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, 8 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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