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Revision 1.75 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 8 19:31:02 2008 UTC (11 years, 10 months ago) by arodri7
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_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_release_2008_09_29
Changes since 1.74: +1 -1 lines
Diff to previous 1.74
updated and corrected sub new

Revision 1.74 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 17 20:45:23 2008 UTC (11 years, 11 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2008_04_23
Changes since 1.73: +2 -4 lines
Diff to previous 1.73
Introduce get_figfam_data().

Revision 1.73 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 12 11:34:03 2008 UTC (11 years, 11 months ago) by overbeek
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Changes since 1.72: +35 -12 lines
Diff to previous 1.72
fixes to figfam function resetting

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Fri Apr 11 14:15:15 2008 UTC (11 years, 11 months ago) by overbeek
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Changes since 1.71: +15 -6 lines
Diff to previous 1.71
changes to FIGfams

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Sat Mar 1 15:37:39 2008 UTC (12 years ago) by overbeek
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Changes since 1.70: +2 -2 lines
Diff to previous 1.70
change ::data/FigfamsData to ::FigfamsData

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Sat Jan 26 01:22:56 2008 UTC (12 years, 2 months ago) by overbeek
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Changes since 1.69: +70 -18 lines
Diff to previous 1.69
FIGfam update

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Thu Dec 6 13:48:31 2007 UTC (12 years, 3 months ago) by parrello
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Changes since 1.68: +42 -42 lines
Diff to previous 1.68
Changed POD format for better compatability with Wiki.

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Fri Nov 16 14:19:38 2007 UTC (12 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.67: +6 -5 lines
Diff to previous 1.67
major fixes to FigFams.pm, FigFam.pm, FFs.pm and FF.pm

Revision 1.67 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 15 16:44:09 2007 UTC (12 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.66: +0 -2 lines
Diff to previous 1.66
fix rep in FigFam.pm

Revision 1.66 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 15 16:37:54 2007 UTC (12 years, 4 months ago) by overbeek
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Changes since 1.65: +1 -1 lines
Diff to previous 1.65
use fgrep rather than grep to extract hdrs

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Thu Nov 15 14:30:50 2007 UTC (12 years, 4 months ago) by overbeek
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Changes since 1.64: +45 -202 lines
Diff to previous 1.64
redone FIGfam stuff

Revision 1.64 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 24 14:25:28 2007 UTC (12 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.63: +10 -11 lines
Diff to previous 1.63
add families_imlementing_role to FigFams.pm

Revision 1.63 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 18 03:27:35 2007 UTC (12 years, 5 months ago) by overbeek
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Changes since 1.62: +26 -9 lines
Diff to previous 1.62
fixes to test_figfam_placement

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Sat Oct 13 15:10:06 2007 UTC (12 years, 5 months ago) by overbeek
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Changes since 1.61: +77 -4 lines
Diff to previous 1.61
fixes to fc_figfams

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Thu Oct 4 00:58:56 2007 UTC (12 years, 5 months ago) by overbeek
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Changes since 1.60: +6 -3 lines
Diff to previous 1.60
check figfams fixes

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Sun Sep 16 14:54:22 2007 UTC (12 years, 6 months ago) by overbeek
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Changes since 1.59: +7 -5 lines
Diff to previous 1.59
code to check figfams on a cluster

Revision 1.59 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Sep 15 22:33:31 2007 UTC (12 years, 6 months ago) by overbeek
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Changes since 1.58: +1 -1 lines
Diff to previous 1.58
FIGfams are now broadened to include PEGs with mismatching functions

Revision 1.58 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 10 19:32:22 2007 UTC (12 years, 8 months ago) by olson
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Changes since 1.57: +1 -1 lines
Diff to previous 1.57
Some minor mg assignment fixes

Revision 1.57 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jul 1 16:22:17 2007 UTC (12 years, 9 months ago) by overbeek
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Changes since 1.56: +19 -7 lines
Diff to previous 1.56
minor fixes to FigFams to support FIGO

Revision 1.56 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 28 23:06:21 2007 UTC (12 years, 9 months ago) by gdpusch
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Changes since 1.55: +4 -1 lines
Diff to previous 1.55
Added check to suppress deleted FIDs to &list_members(). -- /gdp

Revision 1.55 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 7 21:18:40 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.54: +2 -2 lines
Diff to previous 1.54
fixes to decision procedure in FigFam.pm

Revision 1.54 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 25 22:55:44 2007 UTC (12 years, 10 months ago) by gdpusch
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Changes since 1.53: +2 -2 lines
Diff to previous 1.53
Minor cosnmetic change. -- /gdp

Revision 1.53 - (view) (download) (as text) (annotate) - [select for diffs]
Sun May 20 02:53:33 2007 UTC (12 years, 10 months ago) by overbeek
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Changes since 1.52: +28 -7 lines
Diff to previous 1.52
fix test for writable built in FigFam.pm

Revision 1.52 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 17 12:42:28 2007 UTC (12 years, 10 months ago) by gdpusch
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Changes since 1.51: +48 -12 lines
Diff to previous 1.51
Added debugging statements. -- /gdp

Revision 1.51 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 14 14:19:16 2007 UTC (12 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.50: +27 -12 lines
Diff to previous 1.50
update FigFam.pm

Revision 1.50 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 10 13:12:02 2007 UTC (12 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.49: +109 -77 lines
Diff to previous 1.49
update FigFam.pm

Revision 1.49 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 7 16:37:54 2007 UTC (12 years, 10 months ago) by overbeek
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Changes since 1.48: +1 -1 lines
Diff to previous 1.48
minor fix in FigFam.pm

Revision 1.48 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 7 16:37:09 2007 UTC (12 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.47: +1 -1 lines
Diff to previous 1.47
do not blow away bad FIGFAM directories -- mark them

Revision 1.47 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 7 16:22:31 2007 UTC (12 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.46: +1 -1 lines
Diff to previous 1.46
stupid error in FigFam.pm

Revision 1.46 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 7 16:14:26 2007 UTC (12 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.45: +6 -0 lines
Diff to previous 1.45
blow away FIGFAMs with less than 2 sequences

Revision 1.45 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 7 00:43:26 2007 UTC (12 years, 10 months ago) by overbeek
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Changes since 1.44: +37 -19 lines
Diff to previous 1.44
add computation of alignments to building FIGFAMS

Revision 1.44 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 28 14:47:53 2007 UTC (12 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.43: +2 -3 lines
Diff to previous 1.43
add best_tree_using_proml_on_cluster

Revision 1.43 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 25 14:21:41 2007 UTC (13 years ago) by overbeek
Branch: MAIN
Changes since 1.42: +2 -2 lines
Diff to previous 1.42
tighten length constraints for figfam matching

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Sun Mar 18 17:25:19 2007 UTC (13 years ago) by overbeek
Branch: MAIN
Changes since 1.41: +5 -2 lines
Diff to previous 1.41
add filter_figfams.pl

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 28 22:33:17 2007 UTC (13 years, 1 month ago) by olson
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Changes since 1.40: +0 -1 lines
Diff to previous 1.40
fix for readonly data

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Thu Feb 22 23:04:51 2007 UTC (13 years, 1 month ago) by mkubal
Branch: MAIN
Changes since 1.39: +16 -0 lines
Diff to previous 1.39
added pegs_of

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 21 16:09:36 2007 UTC (13 years, 1 month ago) by overbeek
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Changes since 1.38: +25 -7 lines
Diff to previous 1.38
Fixes to FigFam.pm

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 20 19:06:36 2007 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.37: +10 -2 lines
Diff to previous 1.37
fixes to retrimming in PHOB.pm

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 20 13:37:32 2007 UTC (13 years, 1 month ago) by overbeek
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Changes since 1.36: +1 -2 lines
Diff to previous 1.36
fix making alignment in FigFam.pm

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 20 13:10:31 2007 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.35: +26 -10 lines
Diff to previous 1.35
fix making alignment in FigFam.pm

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 19 23:29:14 2007 UTC (13 years, 1 month ago) by overbeek
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Changes since 1.34: +0 -1 lines
Diff to previous 1.34
minor fixes to PHOB.pm

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 19 17:30:22 2007 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.33: +1 -0 lines
Diff to previous 1.33
fix bug relating to projected start/end in trimming

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Feb 18 16:04:13 2007 UTC (13 years, 1 month ago) by overbeek
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Changes since 1.32: +0 -3 lines
Diff to previous 1.32
remove debugging messages from FigFam.pm

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Sun Feb 18 15:45:03 2007 UTC (13 years, 1 month ago) by overbeek
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Changes since 1.31: +40 -3 lines
Diff to previous 1.31
fixes to generating kernel alignments for FigFams

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Thu Feb 15 19:19:26 2007 UTC (13 years, 1 month ago) by overbeek
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Changes since 1.30: +186 -13 lines
Diff to previous 1.30
First draft addition of POD documentaion. -- /gdp

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 29 18:59:08 2007 UTC (13 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.29: +26 -0 lines
Diff to previous 1.29
debugged version of bring_tree_up_to_ali

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Tue Dec 26 00:39:51 2006 UTC (13 years, 3 months ago) by overbeek
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Changes since 1.28: +1 -1 lines
Diff to previous 1.28
fix to FigFam method reset_function

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Mon Dec 25 17:14:15 2006 UTC (13 years, 3 months ago) by overbeek
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Changes since 1.27: +32 -16 lines
Diff to previous 1.27
changes to support updating FIGfam functions

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Wed Nov 15 19:10:40 2006 UTC (13 years, 4 months ago) by olson
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Changes since 1.26: +2 -2 lines
Diff to previous 1.26
fixes for 48hr server

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Wed Oct 18 06:22:27 2006 UTC (13 years, 5 months ago) by overbeek
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Changes since 1.25: +9 -0 lines
Diff to previous 1.25
Added &list_members() method. -- /gdp

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Mon Oct 16 01:31:33 2006 UTC (13 years, 5 months ago) by overbeek
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Changes since 1.24: +5 -3 lines
Diff to previous 1.24
handle invalid family id gracefully in FikgFam.pm

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Fri Oct 13 14:57:55 2006 UTC (13 years, 5 months ago) by overbeek
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Changes since 1.23: +2 -2 lines
Diff to previous 1.23
Minor cosmetic change. -- /gdp

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Thu Oct 12 17:57:10 2006 UTC (13 years, 5 months ago) by overbeek
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Changes since 1.22: +1 -1 lines
Diff to previous 1.22
Temporarily removed check against fused candidate sequence, since it falsely rejects ORFs. -- /gdp

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Thu Oct 5 00:21:21 2006 UTC (13 years, 5 months ago) by overbeek
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Changes since 1.21: +1 -1 lines
Diff to previous 1.21
Minor cosmetic changes. -- /gdp

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 4 19:40:43 2006 UTC (13 years, 5 months ago) by overbeek
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Changes since 1.20: +1 -1 lines
Diff to previous 1.20
Inserted forgotten "FIG::" before call to "flatten_dumper"... :-( -- /gdp

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Wed Oct 4 18:57:19 2006 UTC (13 years, 5 months ago) by overbeek
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Changes since 1.19: +1 -1 lines
Diff to previous 1.19
Added routine to "flatten" Data::Dumper format. -- /gdp

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Sun Oct 1 22:19:24 2006 UTC (13 years, 5 months ago) by overbeek
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Changes since 1.18: +16 -13 lines
Diff to previous 1.18
Modified to return all FigFam sims, not just the top 10. -- /gdp

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Wed Sep 13 23:20:54 2006 UTC (13 years, 6 months ago) by overbeek
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Changes since 1.17: +9 -11 lines
Diff to previous 1.17
fix to FigFam.pm to handle messed up functions

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Sat Sep 2 12:37:00 2006 UTC (13 years, 6 months ago) by overbeek
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Changes since 1.16: +1 -1 lines
Diff to previous 1.16
fix minor error in find_genes_based_on_neighbors

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Tue May 30 02:50:58 2006 UTC (13 years, 10 months ago) by overbeek
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Changes since 1.15: +5 -1 lines
Diff to previous 1.15
fixs to rapid propagation

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Mon May 29 18:07:44 2006 UTC (13 years, 10 months ago) by overbeek
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Changes since 1.14: +3 -2 lines
Diff to previous 1.14
set up find_neighbors to handle existing genomes

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Sun May 21 18:40:30 2006 UTC (13 years, 10 months ago) by overbeek
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Changes since 1.13: +3 -3 lines
Diff to previous 1.13
change bounds check for rapid propagation

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Thu May 18 12:27:21 2006 UTC (13 years, 10 months ago) by overbeek
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Changes since 1.12: +1 -1 lines
Diff to previous 1.12
add normalizded bit scores to BBHs

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Sun May 7 11:57:20 2006 UTC (13 years, 10 months ago) by overbeek
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Changes since 1.11: +1 -1 lines
Diff to previous 1.11
minor degging change for FigFam.pm

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Sun May 7 04:03:10 2006 UTC (13 years, 10 months ago) by overbeek
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Changes since 1.10: +24 -0 lines
Diff to previous 1.10
add new_versions_of_features

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Wed May 3 13:18:22 2006 UTC (13 years, 10 months ago) by overbeek
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Changes since 1.9: +10 -6 lines
Diff to previous 1.9
 update genome parameters in default assignments

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Wed Apr 26 21:57:23 2006 UTC (13 years, 11 months ago) by overbeek
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Changes since 1.8: +5 -3 lines
Diff to previous 1.8
fix building FigFamData

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Wed Apr 12 13:10:38 2006 UTC (13 years, 11 months ago) by overbeek
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Changes since 1.7: +66 -14 lines
Diff to previous 1.7
fixes to making assignments based on consistency

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Tue Apr 4 17:07:49 2006 UTC (13 years, 11 months ago) by overbeek
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Changes since 1.6: +32 -5 lines
Diff to previous 1.6
minor fixes to FigFam

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Mon Apr 3 19:28:52 2006 UTC (13 years, 11 months ago) by overbeek
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Changes since 1.5: +54 -24 lines
Diff to previous 1.5
updates to ARPP/STAG

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Sat Apr 1 18:24:23 2006 UTC (14 years ago) by overbeek
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Changes since 1.4: +9 -3 lines
Diff to previous 1.4
fixes and errors to STAG

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Fri Mar 31 19:37:40 2006 UTC (14 years ago) by overbeek
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Changes since 1.3: +42 -12 lines
Diff to previous 1.3
next version of the STAG code

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Sat Mar 25 23:12:56 2006 UTC (14 years ago) by overbeek
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Changes since 1.2: +143 -14 lines
Diff to previous 1.2
add very buggy start of NewGenome.pm and FigFam stuff

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Tue Mar 21 15:53:30 2006 UTC (14 years ago) by overbeek
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Changes since 1.1: +1 -1 lines
Diff to previous 1.1
fixes to split_and_trim

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Wed Mar 1 20:10:56 2006 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
add FigFam stuff

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