pkgsrc/biology
cube 7e470db80b Update to version 3.15. From David Price in PR#28305.
3.05 - Added -k option to show-coords to only display the best frame for
       overlapping PROmer alignments. Added --[no]optimize option to nucmer
       and promer to allow alignment score optimization to be turned off, i.e
       allow alignments to extend to the ends of sequences rather than
       backtracking to optimize the alignment score. Updated docs.
3.06 - Added -F and -h option to mummer. Changed -mumcand option to
       -mumreference, but left deprecated -mumcand option available. Added
       -maxmatch option to mummer, and changed default behavior of all
       applicable programs to -mumreference (nucmer, promer and mummer).
       Added -w (screen width) option to show-aligns. Updated documentation
       with all of these changes.
3.07 - Added the 'mapview' plotting utility and appropriate documentation.
       Fixed origin wrap shadowing bug in show-tiling when using the -c option.
       NUCmer and PROmer now convert to absolute paths to avoid ambiguity.
3.08 - Added MUMmer examples web docs which gives brief walkthroughs
3.10 - Now Mac OSX compatible. Added -R option to show-tiling.
3.11 - Fixed bug show-tiling -R option. Added some mapview changes. Fixed
       the issue with mummerplot being to faint.
3.12 - Added the --nosimplify option to nucmer for repeat searching. Fixed
       a bug in nucmer and promer. Fixed rounding issue in show-coords.
       Updated citations.
3.13 - Added -d, -g, -G and -o options to show-coords and updated documentation.
       Fixed bug in show-tiling -R
3.14 - Fixed gcc3 compilation bug
3.15 - Fixed --nooptimize in nuc/promer.
2004-12-05 15:24:54 +00:00
..
bioperl Convert to buildlink3. 2004-04-11 03:50:56 +00:00
chemtool Libtool fix for PR pkg/26633, and other issues. Update libtool to 1.5.10 2004-10-03 00:12:51 +00:00
clustalw Rename ALL_TARGET to BUILD_TARGET for consistency with other *_TARGETs. 2004-12-03 15:14:50 +00:00
coalesce Rename ALL_TARGET to BUILD_TARGET for consistency with other *_TARGETs. 2004-12-03 15:14:50 +00:00
fastDNAml Update fastDNAml to version 1.2.2. Notable changes include: 2004-08-16 23:45:59 +00:00
fluctuate Rename ALL_TARGET to BUILD_TARGET for consistency with other *_TARGETs. 2004-12-03 15:14:50 +00:00
genesplicer Convert to buildlink3. 2004-04-11 03:50:56 +00:00
glimmer Update to glimmer-2.13, thanks to cngo@nmsu.edu. 2004-08-19 16:47:01 +00:00
gp Modify patch-aa to replace -e tests with -d tests, so install will work 2004-08-23 14:41:06 +00:00
hmmer Update hmmer to 2.3.2. Patch provided by David Price in PR pkg/28483. 2004-12-01 04:01:09 +00:00
mummer Update to version 3.15. From David Price in PR#28305. 2004-12-05 15:24:54 +00:00
nut Rename ALL_TARGET to BUILD_TARGET for consistency with other *_TARGETs. 2004-12-03 15:14:50 +00:00
pdbalign Move WRKSRC definition away from the first paragraph in a Makefile. 2004-01-20 12:07:06 +00:00
phylip Update phylip to version 3.61. No ChangeLog included. However there is a 2004-08-16 23:58:35 +00:00
profit Rename ALL_TARGET to BUILD_TARGET for consistency with other *_TARGETs. 2004-12-03 15:14:50 +00:00
puzzle Add trailing / on HOMEPAGEs 2003-12-30 17:21:54 +00:00
rasmol Convert to buildlink3. 2004-04-11 04:07:05 +00:00
sewer Do not install files not specified in PLIST. 2004-02-18 21:13:48 +00:00
stride Update HOMEPAGE, addresses PR#26667 from Georg Schwarz. 2004-08-15 13:37:24 +00:00
xylem Convert to buildlink3. 2004-04-11 04:07:05 +00:00
Makefile Add/enable xylem 2003-10-04 19:16:29 +00:00