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Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 17 20:23:35 2010 UTC (9 years, 2 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2010_0928, rast_rel_2010_1206
Changes since 1.22: +0 -1 lines
Diff to previous 1.22 , to selected 1.7
get rid of Dumper

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 17 20:18:15 2010 UTC (9 years, 2 months ago) by golsen
Branch: MAIN
Changes since 1.21: +5 -6 lines
Diff to previous 1.21 , to selected 1.7
Bug fixes in oligomer_similarity().

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 17 20:04:05 2010 UTC (9 years, 2 months ago) by golsen
Branch: MAIN
Changes since 1.20: +62 -0 lines
Diff to previous 1.20 , to selected 1.7
Add code for similarity at any arbitary oligo size.

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Aug 29 22:13:28 2010 UTC (9 years, 3 months ago) by golsen
Branch: MAIN
Changes since 1.19: +200 -20 lines
Diff to previous 1.19 , to selected 1.7
Much code clean-up and consolidation.

New version of add to alignment that does much better gap placement.

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 21 17:29:14 2010 UTC (9 years, 3 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2010_0827
Changes since 1.18: +30 -2 lines
Diff to previous 1.18 , to selected 1.7
Add a pack sequences function, and allow * in a packed sequence (stop).

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Aug 15 23:51:00 2010 UTC (9 years, 3 months ago) by golsen
Branch: MAIN
Changes since 1.17: +32 -20 lines
Diff to previous 1.17 , to selected 1.7
Minor style updates.
Add the ability of read_fasta() to interpret a reference to a sting as
a fasta format string.
use gjoseqlib; $s=join("",<>); @seq=read_fasta(\$s); print_alignment_as_fasta(\@seq);
will echo sequences from stdin.

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 18 20:01:14 2010 UTC (9 years, 10 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2010_0118, rast_rel_2010_0526
Changes since 1.16: +72 -2 lines
Diff to previous 1.16 , to selected 1.7
Add new function for assessing similarity of aligned sequences.
Fix a bug in print fasta when sequence function is undefined under -w.

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 24 21:22:46 2009 UTC (10 years ago) by olson
Branch: MAIN
Changes since 1.15: +2 -0 lines
Diff to previous 1.15 , to selected 1.7
Add more modules to the SAS toolkit.

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 13 18:42:53 2009 UTC (10 years, 8 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2009_05_18, rast_rel_2009_07_09, rast_rel_2009_0925
Changes since 1.14: +51 -6 lines
Diff to previous 1.14 , to selected 1.7
Improve the comments and descriptions of functions.

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 5 14:50:43 2009 UTC (10 years, 10 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2009_03_26
Changes since 1.13: +10 -17 lines
Diff to previous 1.13 , to selected 1.7
fixes to support search for rRNAs

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 12 20:08:01 2008 UTC (11 years, 10 months ago) by golsen
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_release_2008_09_29
Changes since 1.12: +1 -1 lines
Diff to previous 1.12 , to selected 1.7
Fixed major error in read_fasta() when there is not definition.

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 11 20:37:27 2008 UTC (11 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.11: +167 -49 lines
Diff to previous 1.11 , to selected 1.7
Fix a bug in translation with user-supplied genetic code (thank you Gordon).
Fix a bug in read_next_fasta_seq() that failed when the fasta header line
had an id, a space, and then no description.
Improve flexibility of read_next_fasta_seq() so that it will take a file
name, a file handle, or default to STDIN.
Double the speed of read_fasta by reading the whole file, then splitting
it into the structures.

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 3 21:36:41 2008 UTC (11 years, 11 months ago) by golsen
Branch: MAIN
Changes since 1.10: +169 -0 lines
Diff to previous 1.10 , to selected 1.7
Add routines for calculating the fractional sequence difference in a
nucleotide alignment.  They sould be much faster than a loop over
pairs of positions, and allow separate weighting of gap openning and
gap extension, and of terminal versus interal gaps.

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 23 00:33:31 2007 UTC (12 years ago) by golsen
Branch: MAIN
Changes since 1.9: +208 -215 lines
Diff to previous 1.9 , to selected 1.7
Add support for pyrrolysyl proteins.  Also, major revision and clean-up
of the translation utilities in gjoseqlib.pm.

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 1 20:07:42 2007 UTC (12 years, 1 month ago) by golsen
Branch: MAIN
Changes since 1.8: +72 -6 lines
Diff to previous 1.8 , to selected 1.7
Add new subsequence subroutines.

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 26 15:20:16 2007 UTC (12 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.7: +2 -1 lines
Diff to previous 1.7
minor fixes

Revision 1.7 - (view) (download) (as text) (annotate) - [selected]
Sun Jun 10 17:34:54 2007 UTC (12 years, 6 months ago) by golsen
Branch: MAIN
Changes since 1.6: +96 -3 lines
Diff to previous 1.6
Remove dependency on gjolib.pm
Add function to read a sequencing quality score file.

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 10 17:24:38 2007 UTC (12 years, 6 months ago) by golsen
Branch: MAIN
Changes since 1.5: +8 -2 lines
Diff to previous 1.5 , to selected 1.7
Add just a little more usage information for pack_alignment()

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 10 17:17:40 2007 UTC (12 years, 6 months ago) by golsen
Branch: MAIN
Changes since 1.4: +39 -0 lines
Diff to previous 1.4 , to selected 1.7
Add a pack_alignment function.

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 15 00:09:52 2006 UTC (12 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.3: +597 -227 lines
Diff to previous 1.3 , to selected 1.7
add ability to insert sequences into a tree

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 5 19:06:30 2005 UTC (14 years ago) by olson
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
Changes since 1.2: +17 -0 lines
Diff to previous 1.2 , to selected 1.7
Added license words.

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 30 18:33:41 2005 UTC (14 years ago) by golsen
Branch: MAIN
Changes since 1.1: +476 -90 lines
Diff to previous 1.1 , to selected 1.7
This package is not currently used by any scripts, but I anticipate doing
so.  I had not been keeping the FIG version up-to-date relative to my
own.

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 1 16:54:26 2003 UTC (16 years ago) by efrank
Branch: MAIN
Branch point for: initial
Diff to selected 1.7
Initial revision

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