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177c8291a7
implementation of genome scale analyses. The library contains a variety of useful modules, but the particular strengths are: Classes for reading and working with genome-scale multiple local alignments (in MAF, AXT, and LAV formats). Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; optomized for use over network filesystems). Data structures for working with intervals on sequences: * "Binned bitsets" which act just like chromosome sized bit arrays, but lazily allocate regions and allow large blocks of all set or all unset bits to be stored compactly * "Intersecter" for performing fast intersection tests that preserve both query and target intervals and associated annotation WWW: https://github.com/bxlab/bx-python PR: 218757 Submitted by: Yuri Victorovich <yuri@rawbw.com>
116 lines
2.5 KiB
Makefile
116 lines
2.5 KiB
Makefile
# $FreeBSD$
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#
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COMMENT = Biology
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SUBDIR += ariadne
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SUBDIR += artemis
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SUBDIR += avida
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SUBDIR += babel
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SUBDIR += bcftools
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SUBDIR += bedtools
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SUBDIR += biococoa
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SUBDIR += biojava
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SUBDIR += blat
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SUBDIR += bowtie
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SUBDIR += bowtie2
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SUBDIR += bwa
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SUBDIR += cd-hit
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SUBDIR += cdbfasta
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SUBDIR += chemeq
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SUBDIR += clustalw
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SUBDIR += consed
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SUBDIR += crux
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SUBDIR += diamond
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SUBDIR += emboss
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SUBDIR += fasta
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SUBDIR += fasta3
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SUBDIR += fastdnaml
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SUBDIR += fastool
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SUBDIR += fasttree
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SUBDIR += fastx-toolkit
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SUBDIR += fluctuate
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SUBDIR += garlic
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SUBDIR += gff2ps
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SUBDIR += gmap
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SUBDIR += gperiodic
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SUBDIR += grappa
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SUBDIR += hmmer
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SUBDIR += htslib
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SUBDIR += iolib
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SUBDIR += jalview
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SUBDIR += jellyfish
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SUBDIR += lagan
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SUBDIR += lamarc
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SUBDIR += libgtextutils
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SUBDIR += libsbml
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SUBDIR += linux-foldingathome
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SUBDIR += mafft
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SUBDIR += mapm3
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SUBDIR += migrate
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SUBDIR += molden
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SUBDIR += mopac
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SUBDIR += mrbayes
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SUBDIR += mummer
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SUBDIR += muscle
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SUBDIR += ncbi-blast+
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SUBDIR += ncbi-toolkit
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SUBDIR += njplot
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SUBDIR += p5-AcePerl
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SUBDIR += p5-Bio-ASN1-EntrezGene
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SUBDIR += p5-Bio-Coordinate
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SUBDIR += p5-Bio-Das
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SUBDIR += p5-Bio-Das-Lite
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SUBDIR += p5-Bio-GFF3
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SUBDIR += p5-Bio-Glite
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SUBDIR += p5-Bio-Graphics
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SUBDIR += p5-Bio-MAGETAB
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SUBDIR += p5-Bio-NEXUS
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SUBDIR += p5-Bio-Phylo
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SUBDIR += p5-Bio-SCF
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SUBDIR += p5-BioPerl
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SUBDIR += p5-BioPerl-Run
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SUBDIR += p5-transdecoder
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SUBDIR += paml
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SUBDIR += phrap
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SUBDIR += phred
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SUBDIR += phylip
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SUBDIR += phyml
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SUBDIR += plink
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SUBDIR += plinkseq
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SUBDIR += primer3
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SUBDIR += protomol
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SUBDIR += psi88
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SUBDIR += py-biom-format
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SUBDIR += py-biopython
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SUBDIR += py-bx-python
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SUBDIR += py-pysam
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SUBDIR += pycogent
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SUBDIR += pyfasta
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SUBDIR += python-nexus
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SUBDIR += recombine
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SUBDIR += ruby-bio
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SUBDIR += rubygem-bio
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SUBDIR += samtools
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SUBDIR += seaview
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SUBDIR += seqan
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SUBDIR += seqan-apps
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SUBDIR += seqan1
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SUBDIR += seqio
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SUBDIR += seqtools
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SUBDIR += sim4
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SUBDIR += slclust
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SUBDIR += ssaha
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SUBDIR += tRNAscan-SE
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SUBDIR += t_coffee
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SUBDIR += tinker
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SUBDIR += treepuzzle
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SUBDIR += trimmomatic
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SUBDIR += ugene
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SUBDIR += vcftools
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SUBDIR += velvet
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SUBDIR += wise
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SUBDIR += xmolwt
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.include <bsd.port.subdir.mk>
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