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freebsd-ports/biology
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Ion-Mihai Tetcu 9da018b5cc Update biology/ncbi-toolkit to the latest release. 
Quoting from www.ncbi.nlm.nih.gov/blast/blast_whatsnew.shtml
Major changes include:
 blastall now uses the new engine by default, resulting
 in significant performance improvements and enabling
 query concatenation for all program types.

PR:		ports/98570
Submitted by:	maintainer
Approved by:	lawrance (mentor, implict)
2006-06-06 12:05:19 +00:00
..
ariadne Remove USE_REINPLACE from all categories starting with B 2006-05-03 23:26:35 +00:00
artemis - Fix fetch problems 2005-12-05 16:57:26 +00:00
avida Remove USE_REINPLACE from all categories starting with B 2006-05-03 23:26:35 +00:00
babel - Add SHA256 2005-11-24 00:04:00 +00:00
belvu Add belvu 2.29, a viewer for multiple sequence alignments. 2006-03-15 10:24:57 +00:00
biojava BROKEN: Does not compile 2006-04-22 22:10:17 +00:00
blast - Update to 2.0.20060101 2006-01-14 19:36:19 +00:00
blat Add blat 33, a fast tool for local sequence similarity searches. 2006-03-15 10:26:12 +00:00
chemeq - Resurrect, update to version 1.5 (literally 1.50 since I wanted to avoid 2006-01-19 19:47:59 +00:00
clustalw SHA256ify 2006-01-22 08:34:46 +00:00
coalesce - Add SHA256 2005-11-24 00:04:00 +00:00
crimap Remove USE_REINPLACE from all categories starting with B 2006-05-03 23:26:35 +00:00
distribfold Remove USE_REINPLACE from all categories starting with B 2006-05-03 23:26:35 +00:00
dna-qc Remove USE_REINPLACE from all categories starting with B 2006-05-03 23:26:35 +00:00
dotter Add dotter 20021204 # last modified date in FTP server, a viewer for 2006-03-15 10:35:24 +00:00
embassy For EMBOSS: 2006-03-31 09:43:21 +00:00
emboss For EMBOSS: 2006-03-31 09:43:21 +00:00
fasta Update to 21.u1.d1 (fixes fetch). 2006-05-07 13:04:20 +00:00
fasta3 - Update to 34.t25.d8 [1] 2006-06-05 21:18:23 +00:00
fastdnaml - Add SHA256 2005-11-24 00:04:00 +00:00
finchtv SHA256ify 2006-01-22 08:34:46 +00:00
fluctuate - Add SHA256 2005-11-24 00:04:00 +00:00
garlic Remove USE_REINPLACE from all categories starting with B 2006-05-03 23:26:35 +00:00
genpak - Add SHA256 2005-11-24 00:04:00 +00:00
gff2ps Remove USE_REINPLACE from all categories starting with B 2006-05-03 23:26:35 +00:00
gperiodic Remove USE_REINPLACE from all categories starting with B 2006-05-03 23:26:35 +00:00
grappa Remove USE_REINPLACE from all categories starting with B 2006-05-03 23:26:35 +00:00
hmmer SHA256ify 2006-01-22 08:34:46 +00:00
jalview Jalview is a multiple alignment editor written in Java. It is used widely in a 2006-02-13 09:42:13 +00:00
kinemage Reset jeremy@external.org who has not responded to email asking about 2006-04-05 05:46:33 +00:00
L-Breeder Remove USE_REINPLACE from all categories starting with B 2006-05-03 23:26:35 +00:00
lagan Add lagan 1.2, efficient tools for large-scale multiple alignments of 2006-03-16 22:31:26 +00:00
lamarc
libgenome Remove USE_REINPLACE from all categories starting with B 2006-05-03 23:26:35 +00:00
lsysexp - Add MASTER_SITE 2006-06-06 10:07:55 +00:00
mafft - Update to 5.743 2006-03-19 12:59:16 +00:00
migrate Remove USE_REINPLACE from all categories starting with B 2006-05-03 23:26:35 +00:00
molden Remove USE_REINPLACE from all categories starting with B 2006-05-03 23:26:35 +00:00
mopac Reset rmiya@cc.hirosaki-u.ac.jp who has not responded to email asking about 2006-04-05 06:13:46 +00:00
nab SHA256ify 2006-01-22 08:34:46 +00:00
ncbi-toolkit Update biology/ncbi-toolkit to the latest release. 2006-06-06 12:05:19 +00:00
ortep3 Reset rmiya@cc.hirosaki-u.ac.jp who has not responded to email asking about 2006-04-05 06:13:46 +00:00
p5-AcePerl - Update to 1.89 2006-05-02 23:16:02 +00:00
p5-Bio-ASN1-EntrezGene SHA256ify 2006-01-22 08:34:46 +00:00
p5-Bio-Das SHA256ify 2006-01-22 08:34:46 +00:00
p5-Bio-Phylo - Updated from 0.07 to 0.12 2006-05-19 23:18:32 +00:00
p5-bioperl SHA256ify 2006-01-22 08:34:46 +00:00
p5-bioperl-devel Replace ugly "@unexec rmdir %D... 2>/dev/null || true" with @dirrmtry 2006-01-22 01:29:46 +00:00
p5-bioperl-run Bioperl-run contain modules that provides a PERL interface to various 2006-05-02 21:30:08 +00:00
p5-bioperl-run-devel Bioperl-run contain modules that provides a PERL interface to various 2006-05-02 21:31:43 +00:00
paml - Update to 3.15 2006-05-20 18:52:19 +00:00
phylip Put PORTEPOCH back. 2006-02-09 01:17:59 +00:00
platon - Satisfy portlint 2006-05-06 21:20:59 +00:00
povchem Remove USE_REINPLACE from all categories starting with B 2006-05-03 23:26:35 +00:00
primer3 Remove USE_REINPLACE from all categories starting with B 2006-05-03 23:26:35 +00:00
protomol Add protomol 2.0.3, OO, component based, framework for molecular 2006-05-05 20:09:54 +00:00
psi88 Reset rmiya@cc.hirosaki-u.ac.jp who has not responded to email asking about 2006-04-05 06:13:46 +00:00
py-biopython
pymol Remove USE_REINPLACE from all categories starting with B 2006-05-03 23:26:35 +00:00
rasmol - Add SHA256 2005-11-24 00:04:00 +00:00
recombine - Add SHA256 2005-11-24 00:04:00 +00:00
ruby-bio - Update to 1.0.0 2006-04-25 22:09:29 +00:00
seaview - Update to 2006.02.13 2006-04-05 01:58:03 +00:00
seqio SHA256ify 2006-01-22 08:34:46 +00:00
sim4 Remove USE_REINPLACE from all categories starting with B 2006-05-03 23:26:35 +00:00
t_coffee Update to 3.27. 2006-02-10 09:45:28 +00:00
tinker Remove USE_REINPLACE from all categories starting with B 2006-05-03 23:26:35 +00:00
treepuzzle SHA256ify 2006-01-22 08:34:46 +00:00
treeviewx Update to 0.5.1 2005-12-06 02:00:55 +00:00
tRNAscan-SE SHA256ify 2006-01-22 08:34:46 +00:00
wise Remove USE_REINPLACE from all categories starting with B 2006-05-03 23:26:35 +00:00
xdrawchem Remove USE_REINPLACE from all categories starting with B 2006-05-03 23:26:35 +00:00
xmolwt Reset rmiya@cc.hirosaki-u.ac.jp who has not responded to email asking about 2006-04-05 06:13:46 +00:00
Makefile Adding port biology/p5-Bio-Phylo, Phylogenetic analysis using perl. 2006-05-13 16:48:15 +00:00