mirror of
https://git.FreeBSD.org/ports.git
synced 2025-01-26 09:46:09 +00:00
595d0dabcf
The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process. Unlike traditional dynamic programming algorithms that run in quadratic time, the WFA runs in time O(ns+s^2), proportional to the sequence length n and the alignment score s, using O(s^2) memory (or O(s) using the ultralow/BiWFA mode). Moreover, the WFA algorithm exhibits simple computational patterns that the modern compilers can automatically vectorize for different architectures without adapting the code.
245 lines
5.7 KiB
Makefile
245 lines
5.7 KiB
Makefile
COMMENT = Biology
|
|
|
|
SUBDIR += abyss
|
|
SUBDIR += ad2vcf
|
|
SUBDIR += artemis
|
|
SUBDIR += atac-seq
|
|
SUBDIR += augustus
|
|
SUBDIR += avida
|
|
SUBDIR += babel
|
|
SUBDIR += bamtools
|
|
SUBDIR += bamutil
|
|
SUBDIR += barrnap
|
|
SUBDIR += bbmap
|
|
SUBDIR += bcftools
|
|
SUBDIR += bedtools
|
|
SUBDIR += bfc
|
|
SUBDIR += bio-mocha
|
|
SUBDIR += bioawk
|
|
SUBDIR += biococoa
|
|
SUBDIR += biolibc
|
|
SUBDIR += biolibc-tools
|
|
SUBDIR += bioparser
|
|
SUBDIR += biosig
|
|
SUBDIR += biosoup
|
|
SUBDIR += biostar-tools
|
|
SUBDIR += bolt-lmm
|
|
SUBDIR += bowtie
|
|
SUBDIR += bowtie2
|
|
SUBDIR += bwa
|
|
SUBDIR += canu
|
|
SUBDIR += cd-hit
|
|
SUBDIR += cdbfasta
|
|
SUBDIR += checkm
|
|
SUBDIR += clustal-omega
|
|
SUBDIR += clustalw
|
|
SUBDIR += cufflinks
|
|
SUBDIR += cytoscape
|
|
SUBDIR += ddocent
|
|
SUBDIR += diamond
|
|
SUBDIR += dsr-pdb
|
|
SUBDIR += edlib
|
|
SUBDIR += emboss
|
|
SUBDIR += erminej
|
|
SUBDIR += exonerate
|
|
SUBDIR += fasda
|
|
SUBDIR += fasta
|
|
SUBDIR += fasta3
|
|
SUBDIR += fastahack
|
|
SUBDIR += fastdnaml
|
|
SUBDIR += fastool
|
|
SUBDIR += fastp
|
|
SUBDIR += fastq-trim
|
|
SUBDIR += fastqc
|
|
SUBDIR += fasttree
|
|
SUBDIR += fastx-toolkit
|
|
SUBDIR += figtree
|
|
SUBDIR += flash
|
|
SUBDIR += fluctuate
|
|
SUBDIR += freebayes
|
|
SUBDIR += garlic
|
|
SUBDIR += gatk
|
|
SUBDIR += gcta
|
|
SUBDIR += gemma
|
|
SUBDIR += generand
|
|
SUBDIR += gff2ps
|
|
SUBDIR += gffread
|
|
SUBDIR += gmap
|
|
SUBDIR += gperiodic
|
|
SUBDIR += graphlan
|
|
SUBDIR += groopm
|
|
SUBDIR += haplohseq
|
|
SUBDIR += hhsuite
|
|
SUBDIR += hisat2
|
|
SUBDIR += hmmer
|
|
SUBDIR += htslib
|
|
SUBDIR += hyphy
|
|
SUBDIR += igv
|
|
SUBDIR += infernal
|
|
SUBDIR += iolib
|
|
SUBDIR += iqtree
|
|
SUBDIR += jalview
|
|
SUBDIR += jellyfish
|
|
SUBDIR += kallisto
|
|
SUBDIR += kmcp
|
|
SUBDIR += lamarc
|
|
SUBDIR += libbigwig
|
|
SUBDIR += libcombine
|
|
SUBDIR += libgff
|
|
SUBDIR += libgtextutils
|
|
SUBDIR += libneurosim
|
|
SUBDIR += libnuml
|
|
SUBDIR += libsbml
|
|
SUBDIR += libsedml
|
|
SUBDIR += linux-foldingathome
|
|
SUBDIR += mafft
|
|
SUBDIR += mapm3
|
|
SUBDIR += megahit
|
|
SUBDIR += metaeuk
|
|
SUBDIR += migrate
|
|
SUBDIR += minimap2
|
|
SUBDIR += mmseqs2
|
|
SUBDIR += molden
|
|
SUBDIR += mothur
|
|
SUBDIR += mrbayes
|
|
SUBDIR += mummer
|
|
SUBDIR += muscle
|
|
SUBDIR += ncbi-blast+
|
|
SUBDIR += ncbi-cxx-toolkit
|
|
SUBDIR += ncbi-entrez-direct
|
|
SUBDIR += ncbi-toolkit
|
|
SUBDIR += ncbi-vdb
|
|
SUBDIR += ngs-sdk
|
|
SUBDIR += p5-AcePerl
|
|
SUBDIR += p5-Bio-ASN1-EntrezGene
|
|
SUBDIR += p5-Bio-Cluster
|
|
SUBDIR += p5-Bio-Coordinate
|
|
SUBDIR += p5-Bio-DB-EMBL
|
|
SUBDIR += p5-Bio-DB-NCBIHelper
|
|
SUBDIR += p5-Bio-Das
|
|
SUBDIR += p5-Bio-Das-Lite
|
|
SUBDIR += p5-Bio-FeatureIO
|
|
SUBDIR += p5-Bio-GFF3
|
|
SUBDIR += p5-Bio-Glite
|
|
SUBDIR += p5-Bio-Graphics
|
|
SUBDIR += p5-Bio-MAGETAB
|
|
SUBDIR += p5-Bio-NEXUS
|
|
SUBDIR += p5-Bio-Phylo
|
|
SUBDIR += p5-Bio-SCF
|
|
SUBDIR += p5-Bio-Variation
|
|
SUBDIR += p5-BioPerl
|
|
SUBDIR += p5-BioPerl-Run
|
|
SUBDIR += p5-TrimGalore
|
|
SUBDIR += p5-transdecoder
|
|
SUBDIR += paml
|
|
SUBDIR += pbbam
|
|
SUBDIR += pbseqan
|
|
SUBDIR += peak-classifier
|
|
SUBDIR += pear-merger
|
|
SUBDIR += phrap
|
|
SUBDIR += phred
|
|
SUBDIR += phyml
|
|
SUBDIR += picard-tools
|
|
SUBDIR += plink
|
|
SUBDIR += pooler
|
|
SUBDIR += primer3
|
|
SUBDIR += prodigal
|
|
SUBDIR += prodigy-lig
|
|
SUBDIR += protomol
|
|
SUBDIR += psi88
|
|
SUBDIR += py-Genesis-PyAPI
|
|
SUBDIR += py-PySCeS
|
|
SUBDIR += py-bcbio-gff
|
|
SUBDIR += py-biom-format
|
|
SUBDIR += py-biopython
|
|
SUBDIR += py-biosig
|
|
SUBDIR += py-bx-python
|
|
SUBDIR += py-crossmap
|
|
SUBDIR += py-cutadapt
|
|
SUBDIR += py-deeptools
|
|
SUBDIR += py-deeptoolsintervals
|
|
SUBDIR += py-dna-features-viewer
|
|
SUBDIR += py-dnaio
|
|
SUBDIR += py-ete3
|
|
SUBDIR += py-gffutils
|
|
SUBDIR += py-goatools
|
|
SUBDIR += py-gtfparse
|
|
SUBDIR += py-hits
|
|
SUBDIR += py-libnuml
|
|
SUBDIR += py-libsedml
|
|
SUBDIR += py-loompy
|
|
SUBDIR += py-macs2
|
|
SUBDIR += py-mrcfile
|
|
SUBDIR += py-multiqc
|
|
SUBDIR += py-ont-fast5-api
|
|
SUBDIR += py-orange3-bioinformatics
|
|
SUBDIR += py-orange3-single-cell
|
|
SUBDIR += py-pandas-charm
|
|
SUBDIR += py-py2bit
|
|
SUBDIR += py-pybigwig
|
|
SUBDIR += py-pyfaidx
|
|
SUBDIR += py-pyrodigal
|
|
SUBDIR += py-pysam
|
|
SUBDIR += py-python-libsbml
|
|
SUBDIR += py-pywgsim
|
|
SUBDIR += py-resdk
|
|
SUBDIR += py-scikit-bio
|
|
SUBDIR += py-valerius
|
|
SUBDIR += py-xenaPython
|
|
SUBDIR += pyfasta
|
|
SUBDIR += python-nexus
|
|
SUBDIR += rainbow
|
|
SUBDIR += rampler
|
|
SUBDIR += readseq
|
|
SUBDIR += recombine
|
|
SUBDIR += rna-seq
|
|
SUBDIR += ruby-bio
|
|
SUBDIR += rubygem-bio
|
|
SUBDIR += rubygem-bio-executables
|
|
SUBDIR += rubygem-bio-old-biofetch-emulator
|
|
SUBDIR += rubygem-bio-shell
|
|
SUBDIR += sam2pairwise
|
|
SUBDIR += samtools
|
|
SUBDIR += scrm
|
|
SUBDIR += seaview
|
|
SUBDIR += seqan
|
|
SUBDIR += seqan-apps
|
|
SUBDIR += seqan1
|
|
SUBDIR += seqan3
|
|
SUBDIR += seqio
|
|
SUBDIR += seqkit
|
|
SUBDIR += seqtk
|
|
SUBDIR += sigviewer
|
|
SUBDIR += sim4
|
|
SUBDIR += slclust
|
|
SUBDIR += smithwaterman
|
|
SUBDIR += snpeff
|
|
SUBDIR += spoa
|
|
SUBDIR += sra-tools
|
|
SUBDIR += stacks
|
|
SUBDIR += star
|
|
SUBDIR += stringtie
|
|
SUBDIR += subread
|
|
SUBDIR += tRNAscan-SE
|
|
SUBDIR += tabixpp
|
|
SUBDIR += taxonkit
|
|
SUBDIR += treekin
|
|
SUBDIR += treepuzzle
|
|
SUBDIR += trimadap
|
|
SUBDIR += trimmomatic
|
|
SUBDIR += ucsc-userapps
|
|
SUBDIR += ugene
|
|
SUBDIR += unikmer
|
|
SUBDIR += vcf-split
|
|
SUBDIR += vcf2hap
|
|
SUBDIR += vcflib
|
|
SUBDIR += vcftools
|
|
SUBDIR += velvet
|
|
SUBDIR += viennarna
|
|
SUBDIR += vsearch
|
|
SUBDIR += vt
|
|
SUBDIR += wfa2-lib
|
|
SUBDIR += wise
|
|
|
|
.include <bsd.port.subdir.mk>
|