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Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Oct 3 23:03:57 2010 UTC (9 years, 2 months ago) by golsen
Branch: MAIN
CVS Tags: mgrast_dev_02212011, mgrast_dev_02222011, mgrast_dev_03252011, mgrast_dev_03312011, mgrast_dev_04012011, mgrast_dev_04052011, mgrast_dev_04082011, mgrast_dev_04132011, mgrast_release_3_0, mgrast_release_3_0_1, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_4, myrast_33, rast_rel_2010_1206, rast_rel_2011_0119
Changes since 1.24: +1 -2 lines
Diff to previous 1.24 , to selected 1.22
Change behavior of reroot_tree() to ignore distance if there is only one
node.

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 2 00:01:10 2010 UTC (9 years, 2 months ago) by golsen
Branch: MAIN
Changes since 1.23: +753 -286 lines
Diff to previous 1.23 , to selected 1.22
Added reroot_tree() and several functions to support it.
General code clean-up and efficiency modifications.

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Sep 18 20:10:10 2010 UTC (9 years, 2 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2010_0928
Changes since 1.22: +18 -4 lines
Diff to previous 1.22
Fix descriptions of read_tree and read_trees.

Revision 1.22 - (view) (download) (as text) (annotate) - [selected]
Fri Aug 27 23:34:33 2010 UTC (9 years, 3 months ago) by golsen
Branch: MAIN
Changes since 1.21: +187 -0 lines
Diff to previous 1.21
Add routines to make random trees:
  random_equibranch_tree
  random_ultrametric_tree

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 21 17:12:51 2010 UTC (9 years, 3 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2010_0827
Changes since 1.20: +15 -17 lines
Diff to previous 1.20 , to selected 1.22
Handle a few more bad conditions in a graceful manner.

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 14 23:58:51 2010 UTC (9 years, 3 months ago) by golsen
Branch: MAIN
Changes since 1.19: +44 -2 lines
Diff to previous 1.19 , to selected 1.22
Add routine to produce a standard "name" for a tree, allowing direct
comparision for same topology.

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 13 20:33:16 2010 UTC (9 years, 8 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2010_0526
Changes since 1.18: +1 -2 lines
Diff to previous 1.18 , to selected 1.22
Fixed bug introduced yesterday (a spurious newline).

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 12 20:27:23 2010 UTC (9 years, 8 months ago) by fangfang
Branch: MAIN
Changes since 1.17: +2 -1 lines
Diff to previous 1.17 , to selected 1.22
fixed a small bug in representative_for_profile()

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 24 21:22:46 2009 UTC (10 years ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2010_0118
Changes since 1.16: +2 -0 lines
Diff to previous 1.16 , to selected 1.22
Add more modules to the SAS toolkit.

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 8 01:59:24 2009 UTC (10 years, 3 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2009_0925
Changes since 1.15: +38 -13 lines
Diff to previous 1.15 , to selected 1.22
Add ability to put internal node labels in printer plot trees.
(requires dy >= 2).
Reworked the details of subtree order in aesthetic_newick_tree(). It now
looks better in the case of mulitfurcations.

Revision 1.15 - (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
Changes since 1.14: +29 -1 lines
Diff to previous 1.14 , to selected 1.22
Add and/or update routines to support bootstrapping and bootstrap consensus
trees.
Fix some undefined values revealed by -w flag.

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 7 22:14:22 2009 UTC (10 years, 5 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2009_07_09
Changes since 1.13: +188 -181 lines
Diff to previous 1.13 , to selected 1.22
Improved tree printer-plot graphics. Total redesign.

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 1 00:08:52 2009 UTC (10 years, 5 months ago) by golsen
Branch: MAIN
Changes since 1.12: +315 -58 lines
Diff to previous 1.12 , to selected 1.22
Modifications to support line-drawing character set in tree printer plots.

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 22 19:14:50 2009 UTC (10 years, 5 months ago) by golsen
Branch: MAIN
Changes since 1.11: +200 -47 lines
Diff to previous 1.11 , to selected 1.22
Add functions for midpoint rooting of tree in branch.  Add some additional
error checking on trees.

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Mar 29 05:18:19 2008 UTC (11 years, 8 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 1.22
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, 8 months ago) by golsen
Branch: MAIN
Changes since 1.9: +1 -1 lines
Diff to previous 1.9 , to selected 1.22
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) - [select for diffs]
Sun Feb 11 18:55:44 2007 UTC (12 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.8: +545 -72 lines
Diff to previous 1.8 , to selected 1.22
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
adjacent).

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Feb 11 18:25:48 2007 UTC (12 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.7: +319 -16 lines
Diff to previous 1.7 , to selected 1.22
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 (12 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +188 -34 lines
Diff to previous 1.6 , to selected 1.22
new versions of gjo packages

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 19 18:01:14 2006 UTC (12 years, 11 months ago) by golsen
Branch: MAIN
Changes since 1.5: +1 -1 lines
Diff to previous 1.5 , to selected 1.22
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 (12 years, 11 months ago) by golsen
Branch: MAIN
Changes since 1.4: +182 -10 lines
Diff to previous 1.4 , to selected 1.22
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 ago) by overbeek
Branch: MAIN
Changes since 1.3: +10 -10 lines
Diff to previous 1.3 , to selected 1.22
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 (13 years, 11 months 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 1.22
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 ago) by olson
Branch: MAIN
Changes since 1.1: +17 -0 lines
Diff to previous 1.1 , to selected 1.22
Added license words.

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 30 08:44:26 2005 UTC (14 years ago) by golsen
Branch: MAIN
Diff to selected 1.22
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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