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Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 3 19:29:28 2009 UTC (10 years, 4 months ago) by overbeek
Branch: MAIN
CVS Tags: HEAD, 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_dev_05262011, mgrast_dev_06072011, mgrast_dev_08022011, mgrast_dev_08112011, mgrast_dev_10262011, mgrast_dev_12152011, mgrast_release_3_0, mgrast_release_3_0_1, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_4, mgrast_release_3_1_0, mgrast_release_3_1_1, mgrast_release_3_1_2, mgrast_version_3_2, myrast_33, myrast_rel40, rast_rel_2009_0925, rast_rel_2010_0118, rast_rel_2010_0526, rast_rel_2010_0827, rast_rel_2010_0928, rast_rel_2010_1206, rast_rel_2011_0119, rast_rel_2011_0928, rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.14: +3 -3 lines
Diff to previous 1.14
switch from clustalw to muscle

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: 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_rel_2009_07_09, rast_release_2008_09_29
Changes since 1.13: +68 -0 lines
Diff to previous 1.13
add utilities for computing alignments

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 10 13:12:02 2007 UTC (12 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.12: +1 -1 lines
Diff to previous 1.12
update FigFam.pm

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 7 00:43:26 2007 UTC (12 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.11: +1 -2 lines
Diff to previous 1.11
add computation of alignments to building FIGFAMS

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 3 12:24:31 2007 UTC (12 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.10: +5 -1 lines
Diff to previous 1.10
fixed to comp_MR.cgi and FIGV.pm

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 14 15:57:45 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.9: +2 -0 lines
Diff to previous 1.9
fix to computing kernel

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 14 15:04:31 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.8: +1 -1 lines
Diff to previous 1.8
fix confess in PHOB.pm

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 20 19:06:36 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.7: +22 -20 lines
Diff to previous 1.7
fixes to retrimming in PHOB.pm

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 20 14:05:38 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +1 -1 lines
Diff to previous 1.6
do not write debugging file in PHOB.pm

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 20 13:37:33 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +9 -1 lines
Diff to previous 1.5
fix making alignment in FigFam.pm

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 19 17:30:22 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.4: +20 -8 lines
Diff to previous 1.4
fix bug relating to projected start/end in trimming

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 19 14:43:57 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.3: +26 -0 lines
Diff to previous 1.3
update PHOB.pm

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Feb 18 15:45:03 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.2: +1 -1 lines
Diff to previous 1.2
fixes to generating kernel alignments for FigFams

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 17 17:14:11 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.1: +1 -0 lines
Diff to previous 1.1
add possible_frameshift logic to FIGO.pm

Revision 1.1 - (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
add PHOB.pm to support some phylogeny stuff

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