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Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 30 02:22:52 2010 UTC (9 years, 3 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2010_0928, rast_rel_2010_1206
Changes since 1.30: +2 -1 lines
Diff to previous 1.30
re-redirect nap stdout to /dev/null. here's hoping it works on windows still

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 27 19:23:32 2010 UTC (9 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.29: +2 -2 lines
Diff to previous 1.29
Change threshold

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 23 18:33:11 2010 UTC (9 years, 3 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2010_0827
Changes since 1.28: +108 -24 lines
Diff to previous 1.28
More FS_RAST modes & supporting code for SAS use.

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 21 15:49:45 2010 UTC (9 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.27: +0 -55 lines
Diff to previous 1.27
removing dependencies

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 21 15:43:06 2010 UTC (9 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.26: +17 -16 lines
Diff to previous 1.26
removing dependencies

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 21 15:35:09 2010 UTC (9 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.25: +14 -3 lines
Diff to previous 1.25
fixed dependence on FIG.pm but not FIG_Config.pm

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 21 00:30:33 2010 UTC (9 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.24: +1 -1 lines
Diff to previous 1.24
nasty bug in frameshift correction

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 3 00:20:32 2009 UTC (10 years, 8 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2009_05_18, rast_rel_2009_07_09, rast_rel_2009_0925, rast_rel_2010_0118, rast_rel_2010_0526
Changes since 1.23: +136 -32 lines
Diff to previous 1.23
force frameshifts to be of longer chunks

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 24 17:01:53 2009 UTC (10 years, 8 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2009_03_26
Changes since 1.22: +1 -1 lines
Diff to previous 1.22
fix to get rid of undefined value

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 5 14:33:02 2009 UTC (10 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.21: +37 -33 lines
Diff to previous 1.21
fix contraints on gluing pieces

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 4 01:46:36 2009 UTC (10 years, 10 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2009_02_05
Changes since 1.20: +27 -5 lines
Diff to previous 1.20
fixes to seeing if two pieces can be glued together

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Feb 1 21:05:11 2009 UTC (10 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.19: +6 -6 lines
Diff to previous 1.19
it will catch more now

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Oct 19 23:52:51 2008 UTC (11 years, 1 month ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2, rast_rel_2008_11_24, rast_rel_2008_12_18
Changes since 1.18: +43 -6 lines
Diff to previous 1.18
fixes to detecting consistent fragments

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 12 01:47:15 2008 UTC (11 years, 2 months ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_rel_2008_0625, mgrast_rel_2008_0917, mgrast_rel_2008_0919, mgrast_rel_2008_0923, mgrast_rel_2008_0924, rast_2008_0924, rast_rel_2008_09_29, rast_rel_2008_09_30, rast_rel_2008_10_09, rast_rel_2008_10_29, rast_release_2008_09_29
Changes since 1.17: +2 -2 lines
Diff to previous 1.17
fixes to FIGV.pm, CompareMR.pm and FIG.pm to support comparison of metabolic reconstructions

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jul 5 15:53:08 2008 UTC (11 years, 5 months ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_rel_2008_0806, rast_rel_2008_07_21, rast_rel_2008_08_07
Changes since 1.16: +68 -9 lines
Diff to previous 1.16
fixes to grouping

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 15 13:43:00 2008 UTC (11 years, 5 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2008_06_16, rast_rel_2008_06_18
Changes since 1.15: +67 -8 lines
Diff to previous 1.15
fix to computing locations for frameshifts

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 12 21:42:00 2008 UTC (11 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.14: +6 -6 lines
Diff to previous 1.14
enlarge the fragment of DNA in which a hit is sought

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 3 12:27:41 2008 UTC (11 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.13: +12 -5 lines
Diff to previous 1.13
minor fixes relating to translation code

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 3 12:22:24 2008 UTC (11 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.12: +43 -2 lines
Diff to previous 1.12
fix clean_span - it assumed positive strand

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 13 15:21:41 2008 UTC (11 years, 9 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2008_04_23
Changes since 1.11: +3 -3 lines
Diff to previous 1.11
clean up name conflicts

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 9 14:05:06 2008 UTC (11 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.10: +15 -2 lines
Diff to previous 1.10
fixes for nonstandard genetic code

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 9 02:02:51 2008 UTC (11 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.9: +9 -2 lines
Diff to previous 1.9
fixes to FS_RAST.pm to handle nonstandard genetic codes

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 5 15:35:52 2008 UTC (11 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.8: +2 -2 lines
Diff to previous 1.8
additions to FIGfam maintenance

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 18 14:12:56 2007 UTC (11 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.7: +3 -3 lines
Diff to previous 1.7
require valid starts and stops for frameshift correction

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 16 03:55:43 2007 UTC (11 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +103 -70 lines
Diff to previous 1.6
fixes to frameshift correction

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 8 23:27:10 2007 UTC (12 years ago) by overbeek
Branch: MAIN
Changes since 1.5: +1 -0 lines
Diff to previous 1.5
remove trailing stop codon from translation

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 8 21:20:41 2007 UTC (12 years ago) by overbeek
Branch: MAIN
Changes since 1.4: +64 -20 lines
Diff to previous 1.4
fixes to FS_RAST.pm for frameshift detection

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 3 18:42:17 2007 UTC (12 years ago) by overbeek
Branch: MAIN
Changes since 1.3: +1 -1 lines
Diff to previous 1.3
fix reference to nap in FS_RAST.pm

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 2 18:41:53 2007 UTC (12 years ago) by overbeek
Branch: MAIN
Changes since 1.2: +7 -0 lines
Diff to previous 1.2
fixes to add an extra alignment

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 21 20:41:05 2007 UTC (12 years ago) by overbeek
Branch: MAIN
Changes since 1.1: +150 -54 lines
Diff to previous 1.1
add code to fix frameshifts in a genome

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 21 13:36:05 2007 UTC (12 years ago) by overbeek
Branch: MAIN
add FS_RAST.pm, a module to support RAST searches correcting frameshifts

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