Log of /FigKernelPackages/gjonewicklib.pm
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Revision
1.25 -
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Sun Oct 3 23:03:57 2010 UTC (9 years, 2 months ago) by
golsen
Branch:
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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
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selected 1.7
Change behavior of reroot_tree() to ignore distance if there is only one
node.
Revision
1.11 -
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Sat Mar 29 05:18:19 2008 UTC (11 years, 8 months ago) by
golsen
Branch:
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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
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selected 1.7
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 -
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Mon Apr 9 21:00:24 2007 UTC (12 years, 7 months ago) by
golsen
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Changes since
1.9: +1 -1 lines
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previous 1.9
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selected 1.7
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 -
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Sun Feb 11 18:55:44 2007 UTC (12 years, 9 months ago) by
golsen
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Changes since
1.8: +545 -72 lines
Diff to
previous 1.8
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selected 1.7
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
1.7 -
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Fri Jan 12 23:45:29 2007 UTC (12 years, 10 months ago) by
overbeek
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Changes since
1.6: +188 -34 lines
Diff to
previous 1.6
new versions of gjo packages
Revision
1.1 -
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Wed Nov 30 08:44:26 2005 UTC (14 years ago) by
golsen
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Diff
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selected 1.7
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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