freebsd-ports/biology
Kurt Jaeger 2ed702d2d3 biology/molden: 5.4 -> 5.7
- Adds editable text fields that are longer than the visible string
  and introduces a new way of selecting a range of amino acids.
- introduces interfaces to the open source packages openbabel and pharmer.
  Openbabel is used to create 2D images of the molecules in a .sdf
  file. It is also used to do 2D fingerprint searching.
  Pharmer is used to pharmacophore (3D) searching against indexed
  databases of .sdf files.
2016-08-26 06:00:47 +00:00
..
ariadne Cleanup $() variables in ports Makefiles. 2016-07-20 15:33:20 +00:00
artemis
avida
babel
bcftools
bedtools biology/bedtools is not jobs safe 2016-08-22 04:32:18 +00:00
biococoa
biojava When there is a do-install target, do not use a post-install target, do 2016-07-19 11:04:13 +00:00
blat
bowtie
bowtie2
bwa
cd-hit
cdbfasta
chemeq
clustalw
consed
crux
diamond Update to version 0.8.19 2016-08-25 18:49:12 +00:00
emboss - update libgd to 2.2.2 2016-07-20 09:33:31 +00:00
fasta
fasta3
fastdnaml
fastool
fasttree
fastx-toolkit
fluctuate
garlic
gff2ps
gmap
gperiodic - LICENSE 2016-07-02 09:05:22 +00:00
grappa
hmmer
htslib
iolib
jalview
jellyfish
lagan
lamarc - Switch to options helpers 2016-08-18 09:31:58 +00:00
libgtextutils
libsbml
linux-foldingathome
mafft
mapm3
migrate
molden biology/molden: 5.4 -> 5.7 2016-08-26 06:00:47 +00:00
mopac
mrbayes
mummer
muscle
ncbi-blast+
ncbi-toolkit - Add missing dependency, fixing build 2016-06-24 09:04:45 +00:00
p5-AcePerl
p5-Bio-ASN1-EntrezGene
p5-Bio-Das
p5-Bio-Das-Lite
p5-Bio-GFF3
p5-Bio-Glite
p5-Bio-Graphics
p5-Bio-MAGETAB
p5-Bio-NEXUS
p5-Bio-Phylo
p5-Bio-SCF
p5-bioperl
p5-bioperl-run
p5-transdecoder
paml
phrap
phred
phylip
phyml
plink
plinkseq
primer3
protomol
psi88
py-biom-format - Fix run-time dependency issues 2016-06-11 09:25:04 +00:00
py-biopython
pycogent - Update to 1.9 [1] 2016-08-08 11:21:04 +00:00
pyfasta
python-nexus - Update to 1.35 2016-06-08 07:39:05 +00:00
recombine When there is a do-install target, do not use a post-install target, do 2016-07-19 11:04:13 +00:00
ruby-bio
samtools
seaview biology/seaview: Update version 4.5.4.8=>4.6 2016-06-10 11:06:42 +00:00
seqan
seqan1 When there is a do-install target, do not use a post-install target, do 2016-07-19 11:04:13 +00:00
seqan-apps
seqio
seqtools biology/seqtools: 4.42.1 -> 4.43.0 2016-07-31 14:19:09 +00:00
sim4
slclust
ssaha
t_coffee
tinker
treepuzzle
treeviewx
trimmomatic
tRNAscan-SE
ugene
vcftools
velvet
wise - Switch to options helpers 2016-06-21 09:05:06 +00:00
xmolwt
Makefile Remove expired ports without open PRs: 2016-07-04 20:48:23 +00:00