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Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 5 21:24:50 2011 UTC (9 years, 2 months ago) by golsen
Branch: MAIN
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_dev_05262011, mgrast_dev_06072011, mgrast_dev_08022011, mgrast_dev_08112011, 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, myrast_33, myrast_rel40
Changes since 1.17: +309 -339 lines
Diff to previous 1.17 , to selected 1.13
Huge restructuring of the rep_seq() and rep_seq2() functions.  Better performance.
Fixed a bug in the order by sequence length option.

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 7 00:40:42 2010 UTC (9 years, 4 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2011_0119
Changes since 1.16: +111 -164 lines
Diff to previous 1.16 , to selected 1.13
Many updates to make better use of SeedAware.pm.

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 8 19:08:52 2010 UTC (9 years, 5 months ago) by fangfang
Branch: MAIN
CVS Tags: rast_rel_2010_1206
Changes since 1.15: +4 -4 lines
Diff to previous 1.15 , to selected 1.13
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, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.14: +1 -1 lines
Diff to previous 1.14 , to selected 1.13
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, 6 months 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) - [selected]
Wed Sep 29 18:41:49 2010 UTC (9 years, 6 months 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 (10 years 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 , to selected 1.13
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 (10 years, 2 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2010_0118
Changes since 1.10: +6 -8 lines
Diff to previous 1.10 , to selected 1.13
Minor changes in style.

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 18 19:32:15 2009 UTC (10 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.9: +2 -0 lines
Diff to previous 1.9 , to selected 1.13
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, 11 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 , to selected 1.13
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, 11 months ago) by golsen
Branch: MAIN
Changes since 1.7: +27 -3 lines
Diff to previous 1.7 , to selected 1.13
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, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +66 -1 lines
Diff to previous 1.6 , to selected 1.13
add utilities for computing alignments

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 19 20:01:56 2007 UTC (13 years ago) by golsen
Branch: MAIN
Changes since 1.5: +2 -2 lines
Diff to previous 1.5 , to selected 1.13
Fix to error message.

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 19 18:58:10 2007 UTC (13 years ago) by golsen
Branch: MAIN
Changes since 1.4: +667 -318 lines
Diff to previous 1.4 , to selected 1.13
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 (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.3: +0 -1 lines
Diff to previous 1.3 , to selected 1.13
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 (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.2: +6 -3 lines
Diff to previous 1.2 , to selected 1.13
update PHOB.pm

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 16 17:41:34 2007 UTC (13 years, 1 month ago) by golsen
Branch: MAIN
Changes since 1.1: +48 -14 lines
Diff to previous 1.1 , to selected 1.13
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 (13 years, 3 months ago) by golsen
Branch: MAIN
Diff to selected 1.13
Adding representative_sequences.pm

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