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Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 8 19:08:52 2010 UTC (9 years ago) by fangfang
Branch: MAIN
CVS Tags: rast_rel_2010_1206
Changes since 1.15: +4 -4 lines
Diff to previous 1.15
handle undefined return value from pack_sequences in req_seq and rep_seq_2

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 4 21:12:11 2010 UTC (9 years ago) by overbeek
Branch: MAIN
Changes since 1.14: +1 -1 lines
Diff to previous 1.14
handle undefined list issue

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 29 23:59:32 2010 UTC (9 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.13: +17 -0 lines
Diff to previous 1.13
remove indels from sequences

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 29 18:41:49 2010 UTC (9 years, 1 month ago) by fangfang
Branch: MAIN
Changes since 1.12: +48 -4 lines
Diff to previous 1.12
add genome ID list to be kept

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 6 03:36:43 2010 UTC (9 years, 7 months ago) by fangfang
Branch: MAIN
CVS Tags: rast_rel_2010_0526, rast_rel_2010_0827, rast_rel_2010_0928
Changes since 1.11: +6 -4 lines
Diff to previous 1.11
check if formatdb and blastall exist in $FIG_Config::ext_bin

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 19 01:58:52 2010 UTC (9 years, 10 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2010_0118
Changes since 1.10: +6 -8 lines
Diff to previous 1.10
Minor changes in style.

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 18 19:32:15 2009 UTC (9 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.9: +2 -0 lines
Diff to previous 1.9
add as SAS components

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 12 21:22:23 2007 UTC (12 years, 6 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_rel_2009_0925, rast_release_2008_09_29
Changes since 1.8: +2 -0 lines
Diff to previous 1.8
add make_trimmed_alignment_from_ids

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 12 20:47:03 2007 UTC (12 years, 6 months ago) by golsen
Branch: MAIN
Changes since 1.7: +27 -3 lines
Diff to previous 1.7
Modifications to control ordering of sequences in representative sets and
in sequeneces added to an alignment.  Also new options to silently remove
sequences with duplicate ids.

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 12 20:12:56 2007 UTC (12 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +66 -1 lines
Diff to previous 1.6
add utilities for computing alignments

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 19 20:01:56 2007 UTC (12 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.5: +2 -2 lines
Diff to previous 1.5
Fix to error message.

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 19 18:58:10 2007 UTC (12 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.4: +667 -318 lines
Diff to previous 1.4
Change in the representative sequences algorithm.  This could still use
more work.

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 28 21:55:44 2007 UTC (12 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.3: +0 -1 lines
Diff to previous 1.3
remove debugging line from representative_sequences.pm

Revision 1.3 - (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 1.2: +6 -3 lines
Diff to previous 1.2
update PHOB.pm

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 16 17:41:34 2007 UTC (12 years, 9 months ago) by golsen
Branch: MAIN
Changes since 1.1: +48 -14 lines
Diff to previous 1.1
Major improvement in representative_sequences.pl.  Greatly improved
comments in representative_sequences.pm.

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 20 20:49:21 2006 UTC (12 years, 11 months ago) by golsen
Branch: MAIN
Adding representative_sequences.pm

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