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Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Mar 29 05:18:19 2008 UTC (11 years, 10 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, mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2, rast_2008_0924, 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, rast_rel_2008_09_29, rast_rel_2008_09_30, rast_rel_2008_10_09, rast_rel_2008_10_29, rast_rel_2008_11_24, rast_rel_2008_12_18, rast_rel_2009_02_05, rast_rel_2009_03_26, rast_rel_2009_05_18, rast_release_2008_09_29
Changes since 1.10: +21 -6 lines
Diff to previous 1.10 , to selected 1.9
Allow matched [ ... ] inside Newick tree comment.  This violates the standard,
but allows much more flexibility.  It is consistent with the treatment in
programs like PAUP*.

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 9 21:00:24 2007 UTC (12 years, 9 months ago) by golsen
Branch: MAIN
Changes since 1.9: +1 -1 lines
Diff to previous 1.9
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 1.9 - (view) (download) (as text) (annotate) - [selected]
Sun Feb 11 18:55:44 2007 UTC (12 years, 11 months ago) by golsen
Branch: MAIN
Changes since 1.8: +545 -72 lines
Diff to previous 1.8
Added much support for adding sequences to trees.  In particular, the
ability to extract a representative tree defined by the lineages that
originate near a tip, or the current root of the tree.  Also, rerooting
to a point on the branches between 2 nodes (which do not need to be

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Feb 11 18:25:48 2007 UTC (12 years, 11 months ago) by golsen
Branch: MAIN
Changes since 1.7: +319 -16 lines
Diff to previous 1.7 , to selected 1.9
New functions for making big trees.

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 12 23:45:29 2007 UTC (13 years ago) by overbeek
Branch: MAIN
Changes since 1.6: +188 -34 lines
Diff to previous 1.6 , to selected 1.9
new versions of gjo packages

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 19 18:01:14 2006 UTC (13 years, 1 month ago) by golsen
Branch: MAIN
Changes since 1.5: +1 -1 lines
Diff to previous 1.5 , to selected 1.9
Bug fix in passing a file handle reference to printer_plot_newick.

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 19 17:32:48 2006 UTC (13 years, 1 month ago) by golsen
Branch: MAIN
Changes since 1.4: +182 -10 lines
Diff to previous 1.4 , to selected 1.9
Add a few new routines to gjonewicklib.pm

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 15 00:09:52 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.3: +10 -10 lines
Diff to previous 1.3 , to selected 1.9
add ability to insert sequences into a tree

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 3 19:50:32 2006 UTC (14 years ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
Changes since 1.2: +6 -1 lines
Diff to previous 1.2 , to selected 1.9
RAE: Correcting division by zero error

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 5 19:06:30 2005 UTC (14 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.1: +17 -0 lines
Diff to previous 1.1 , to selected 1.9
Added license words.

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 30 08:44:26 2005 UTC (14 years, 2 months ago) by golsen
Branch: MAIN
Diff to selected 1.9
Introduce a different tree printing routine to fid_checked.  This required
a new version of align_with_clustal.pl (= align_with_clustal_2.pl) and a
new tree utilities library (gjonewicklib.pm).

The new tree printer does not require deleting the extra lines (they are
not included in the first place).  This would probably allow some other
restructuring of the code in fid_checked, but I did the minimum.

The other reason for the changes (actually the real reason) is that it is
now possible to introduce midpoint rooting to the tree, and to reorder
the taxa so that the tree is MUCH easier to read (aesthetic tree order).

Also I'm changing it to use a second-generation tree from the alignment,
not just show the guide tree.

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