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Revision 1.53 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 23 21:09:15 2015 UTC (4 years, 4 months ago) by fangfang
Branch: MAIN
CVS Tags: HEAD
Changes since 1.52: +84 -82 lines
Diff to previous 1.52
remove empty sequences in trimmed alignments

Revision 1.52 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 16 16:27:01 2014 UTC (5 years, 6 months ago) by fangfang
Branch: MAIN
Changes since 1.51: +2 -2 lines
Diff to previous 1.51
update raxml

Revision 1.51 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 3 20:40:01 2014 UTC (5 years, 11 months ago) by fangfang
Branch: MAIN
CVS Tags: rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.50: +2 -1 lines
Diff to previous 1.50
add CoreSEED db

Revision 1.50 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 4 18:09:19 2014 UTC (6 years, 2 months ago) by fangfang
Branch: MAIN
Changes since 1.49: +2 -14 lines
Diff to previous 1.49
remove hard-coded paths to alignment tools

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Wed Oct 2 21:51:26 2013 UTC (6 years, 6 months ago) by fangfang
Branch: MAIN
Changes since 1.48: +4 -2 lines
Diff to previous 1.48
update NR with all md5

Revision 1.48 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 2 19:54:05 2013 UTC (6 years, 6 months ago) by fangfang
Branch: MAIN
Changes since 1.47: +2 -2 lines
Diff to previous 1.47
change default db to PUBSEED

Revision 1.47 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 2 19:51:21 2013 UTC (6 years, 6 months ago) by fangfang
Branch: MAIN
Changes since 1.46: +2 -2 lines
Diff to previous 1.46
update NR for all pubseed seqs

Revision 1.46 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 2 19:48:55 2013 UTC (6 years, 6 months ago) by fangfang
Branch: MAIN
Changes since 1.45: +5 -2 lines
Diff to previous 1.45
update NR

Revision 1.45 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 24 02:56:05 2012 UTC (7 years, 6 months ago) by fangfang
Branch: MAIN
Changes since 1.44: +3 -2 lines
Diff to previous 1.44
Make -reorder the default option for mafft alignment.

Revision 1.44 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Sep 23 22:32:04 2012 UTC (7 years, 6 months ago) by fangfang
Branch: MAIN
Changes since 1.43: +3 -2 lines
Diff to previous 1.43
Add default path for clustalw

Revision 1.43 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Sep 23 21:54:17 2012 UTC (7 years, 6 months ago) by fangfang
Branch: MAIN
Changes since 1.42: +153 -0 lines
Diff to previous 1.42
Add signature column analysis

Revision 1.42 - (view) (download) (as text) (annotate) - [select for diffs]
Sun May 13 16:47:03 2012 UTC (7 years, 10 months ago) by fangfang
Branch: MAIN
CVS Tags: mgrast_version_3_2
Changes since 1.41: +2 -1 lines
Diff to previous 1.41
update

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 6 21:09:05 2011 UTC (8 years, 11 months ago) by fangfang
Branch: MAIN
CVS Tags: mgrast_dev_05262011, mgrast_dev_06072011, mgrast_dev_08022011, mgrast_dev_08112011, mgrast_dev_10262011, mgrast_dev_12152011, mgrast_release_3_1_0, mgrast_release_3_1_1, mgrast_release_3_1_2, myrast_rel40, rast_rel_2011_0928
Changes since 1.40: +9 -11 lines
Diff to previous 1.40
fixed bug with aligning seq ends with clustal

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 27 16:40:35 2011 UTC (8 years, 11 months ago) by fangfang
Branch: MAIN
Changes since 1.39: +1 -1 lines
Diff to previous 1.39
fixed bug in trimming

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 27 16:11:05 2011 UTC (8 years, 11 months ago) by fangfang
Branch: MAIN
Changes since 1.38: +33 -9 lines
Diff to previous 1.38
update pubseed db

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Apr 3 16:53:21 2011 UTC (9 years ago) by fangfang
Branch: MAIN
CVS Tags: mgrast_dev_04052011, mgrast_dev_04082011, mgrast_dev_04132011, mgrast_release_3_0_3, mgrast_release_3_0_4
Changes since 1.37: +60 -0 lines
Diff to previous 1.37
added function for extracting conserved regions from alignment

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 23 06:23:05 2011 UTC (9 years ago) by fangfang
Branch: MAIN
CVS Tags: mgrast_dev_03252011, mgrast_dev_03312011, mgrast_dev_04012011, myrast_33
Changes since 1.36: +1 -1 lines
Diff to previous 1.36
update

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 21 04:10:55 2011 UTC (9 years ago) by fangfang
Branch: MAIN
Changes since 1.35: +10 -3 lines
Diff to previous 1.35
update options for make_tree

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 20 06:59:00 2011 UTC (9 years ago) by fangfang
Branch: MAIN
Changes since 1.34: +2 -2 lines
Diff to previous 1.34
fix a bug with aligning 1 seq

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 18 16:17:07 2011 UTC (9 years ago) by fangfang
Branch: MAIN
Changes since 1.33: +20 -7 lines
Diff to previous 1.33
add parallel support for bootstrap

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 18 14:11:33 2011 UTC (9 years ago) by fangfang
Branch: MAIN
Changes since 1.32: +1 -1 lines
Diff to previous 1.32
minor update

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 7 16:23:05 2011 UTC (9 years, 1 month ago) by fangfang
Branch: MAIN
CVS Tags: mgrast_release_3_0, mgrast_release_3_0_1, mgrast_release_3_0_2
Changes since 1.31: +126 -0 lines
Diff to previous 1.31
update

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 25 14:50:35 2011 UTC (9 years, 1 month ago) by fangfang
Branch: MAIN
Changes since 1.30: +1 -2 lines
Diff to previous 1.30
update

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 25 08:43:43 2011 UTC (9 years, 1 month ago) by fangfang
Branch: MAIN
Changes since 1.29: +2 -2 lines
Diff to previous 1.29
update

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 25 08:39:14 2011 UTC (9 years, 1 month ago) by fangfang
Branch: MAIN
Changes since 1.28: +3 -2 lines
Diff to previous 1.28
update bootstrap default

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 21 17:16:40 2011 UTC (9 years, 1 month ago) by fangfang
Branch: MAIN
CVS Tags: mgrast_dev_02212011, mgrast_dev_02222011
Changes since 1.27: +4 -3 lines
Diff to previous 1.27
use vol/public-pseed for psiblast genome database

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 17 04:25:59 2011 UTC (9 years, 1 month ago) by fangfang
Branch: MAIN
Changes since 1.26: +2 -1 lines
Diff to previous 1.26
add ncpu option for pfam_scan()

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 16 20:41:46 2011 UTC (9 years, 1 month ago) by fangfang
Branch: MAIN
Changes since 1.25: +6 -3 lines
Diff to previous 1.25
add nthread option for psiblast_search

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 16 20:14:22 2011 UTC (9 years, 1 month ago) by fangfang
Branch: MAIN
Changes since 1.24: +16 -4 lines
Diff to previous 1.24
add ppseed for psiblast_search

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 29 22:13:49 2010 UTC (9 years, 3 months ago) by fangfang
Branch: MAIN
CVS Tags: rast_rel_2011_0119
Changes since 1.23: +5 -5 lines
Diff to previous 1.23
update default values

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 29 21:50:43 2010 UTC (9 years, 3 months ago) by fangfang
Branch: MAIN
Changes since 1.22: +12 -6 lines
Diff to previous 1.22
update

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 27 15:51:19 2010 UTC (9 years, 3 months ago) by fangfang
Branch: MAIN
Changes since 1.21: +1 -1 lines
Diff to previous 1.21
update pseed.nr

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 27 00:05:14 2010 UTC (9 years, 3 months ago) by fangfang
Branch: MAIN
Changes since 1.20: +305 -7 lines
Diff to previous 1.20
new trimming method and incremental psiblast search

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 13 22:15:26 2010 UTC (9 years, 3 months ago) by fangfang
Branch: MAIN
Changes since 1.19: +57 -4 lines
Diff to previous 1.19
updates

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 29 20:01:30 2010 UTC (9 years, 4 months ago) by fangfang
Branch: MAIN
CVS Tags: rast_rel_2010_1206
Changes since 1.18: +2 -2 lines
Diff to previous 1.18
update comments

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 29 19:50:04 2010 UTC (9 years, 4 months ago) by fangfang
Branch: MAIN
Changes since 1.17: +37 -18 lines
Diff to previous 1.17
update options for psiblast_search

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Nov 27 23:44:11 2010 UTC (9 years, 4 months ago) by fangfang
Branch: MAIN
Changes since 1.16: +15 -4 lines
Diff to previous 1.16
support bootstrapped tree

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Nov 27 00:43:15 2010 UTC (9 years, 4 months ago) by fangfang
Branch: MAIN
Changes since 1.15: +1 -0 lines
Diff to previous 1.15
print psiblast history to STDERR

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Nov 27 00:25:37 2010 UTC (9 years, 4 months ago) by fangfang
Branch: MAIN
Changes since 1.14: +108 -2 lines
Diff to previous 1.14
add incremental_psiblast_search

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 24 04:06:02 2010 UTC (9 years, 4 months ago) by fangfang
Branch: MAIN
Changes since 1.13: +2 -5 lines
Diff to previous 1.13
change psiblast database name

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 17 20:17:07 2010 UTC (9 years, 4 months ago) by fangfang
Branch: MAIN
Changes since 1.12: +8 -4 lines
Diff to previous 1.12
use statements adjustment

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 17 19:42:55 2010 UTC (9 years, 4 months ago) by fangfang
Branch: MAIN
Changes since 1.11: +2 -2 lines
Diff to previous 1.11
support for make_tree

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 17 16:58:18 2010 UTC (9 years, 4 months ago) by fangfang
Branch: MAIN
Changes since 1.10: +50 -3 lines
Diff to previous 1.10
add make_tree

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 16 22:53:28 2010 UTC (9 years, 4 months ago) by fangfang
Branch: MAIN
Changes since 1.9: +3 -2 lines
Diff to previous 1.9
change organism directory

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 12 14:27:28 2010 UTC (9 years, 4 months ago) by fangfang
Branch: MAIN
Changes since 1.8: +4 -2 lines
Diff to previous 1.8
temporary psiblast db

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 11 07:40:20 2010 UTC (9 years, 4 months ago) by fangfang
Branch: MAIN
Changes since 1.7: +279 -172 lines
Diff to previous 1.7
add support for psiblast search

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 10 17:31:40 2010 UTC (9 years, 4 months ago) by fangfang
Branch: MAIN
Changes since 1.6: +2 -2 lines
Diff to previous 1.6
change default alignment tool to Clustal

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 10 16:54:47 2010 UTC (9 years, 4 months ago) by fangfang
Branch: MAIN
Changes since 1.5: +234 -13 lines
Diff to previous 1.5
Updates and bug fixes

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 28 13:13:34 2010 UTC (9 years, 5 months ago) by fangfang
Branch: MAIN
Changes since 1.4: +1 -0 lines
Diff to previous 1.4
bug fix

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 27 21:17:15 2010 UTC (9 years, 5 months ago) by fangfang
Branch: MAIN
Changes since 1.3: +2 -0 lines
Diff to previous 1.3
bug fix

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 27 21:06:39 2010 UTC (9 years, 5 months ago) by fangfang
Branch: MAIN
Changes since 1.2: +7 -2 lines
Diff to previous 1.2
options for e-value and min-identity cutoff

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 27 20:41:18 2010 UTC (9 years, 5 months ago) by fangfang
Branch: MAIN
Changes since 1.1: +70 -1 lines
Diff to previous 1.1
add psiblast profile search

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 27 20:05:30 2010 UTC (9 years, 5 months ago) by fangfang
Branch: MAIN
module for local alignment and tree routines

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