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bioinformatics_catalog

Bioinformatics Software Catalog

Not including OpenHPC and other RPM software in /opt and R/python/perl modules

/share/apps/bioinformatics_Location mod/version Website latest_version
./abyss/abyss-1.3.7 mod/version
./abyss/abyss-1.9.0 mod/version
./abyss/2.0.2 mod/version https://www.bcgsc.ca/resources/software/abyss 2.1.5
./admixture/admixture_linux-1.3.0 mod/version https://bioinformaticshome.com/tools/descriptions/ADMIXTURE.html 1.3.0
./aegean/0.15.1 mod/version https://standage.github.io/AEGeAn/ 0.16.0
./allpaths-lg/51279 mod/version ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/ 52488
./annovar(20180416) annovar/1.0 https://annovar.openbioinformatics.org/en/latest/ 20210123
./astalavista/astalavista-3.2 mod/version http://sammeth.net/confluence/display/ASTA/Home
./ASTRAL(5.7.3) mod/version https://github.com/smirarab/ASTRAL 5.7.3
./augustus/3.22 augustus/3.2.2 http://bioinf.uni-greifswald.de/augustus/ 3.4.9
./b2g4pipe(2.5) mod/version https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/b2g4pipe-2-5 2.5
./BA3-SNPS-autotune(20200825) mod/version https://github.com/stevemussmann/BA3-SNPS-autotune 2.1.2
./bam2fastq/1.1.0 mod/version https://gslweb.discoveryls.com/information/software/bam2fastq 1.1.0
./bamtools/2.4.1 mod/version https://github.com/pezmaster31/bamtools 2.5.1
./BayesAss3-SNPs mod/version https://github.com/stevemussmann/BayesAss3-SNPs 1.1
./bbmap/34.30 bbmap/34.30
./bbmap/38.79 bbmap/38.79
./bbmap/38.82 bbmap/38.82 https://sourceforge.net/projects/bbmap/ 38.9
./bcftools/1.10.2 mod/version https://github.com/samtools/bcftools 1.11
./beagle/2.1.2 mod/version
./beagle/2.4.2 mod/version
./beagle/2.4.2-avx-openmp mod/version
./beagle/2.4.2-sse-openmp mod/version https://faculty.washington.edu/browning/beagle/beagle.html 5.1
./beast/2.4 mod/version
./beast/beast2.4.7 mod/version https://www.beast2.org/ 2.6
./bedtools2/2.25.0 mod/version https://bedtools.readthedocs.io/en/latest/ 2.28
./bfc mod/version https://github.com/lh3/bfc -2014
./bismark/0.23.0 mod/version https://github.com/FelixKrueger/Bismark 0.23.0
./blasr/5.3 blasr/5.3 https://github.com/PacificBiosciences/blasr 5.3.3
./blast/blast-2.2.22 mod/version
./blast/db20150912 mod/version
./blast/ncbi-blast-2.2.29+ mod/version
./blast/ncbi-blast-2.3.0+ mod/version
./blast/ncbi-blast-2.4.0+ mod/version
./blast/ncbi-blast-2.5.0+ mod/version
./blast/ncbi-blast-2.6.0+ mod/version
./blast/ncbi-blast-2.6.0+-src mod/version
./blast/ncbi-blast-2.7.1+ mod/version
./blast/ncbi-blast-2.9.0+ blast/2.9.0+
./blast/ncbi-blast-2.9.0+-src-gcc-sse4a mod/version
./blast/ncbi-blast-2.10.0+ blast/2.10.0+bin
./blast/ncbi-blast-2.10.0+-src-gcc-avx blast/2.10.0+src
./blast/ncbi-blast-2.10.0+-src-gcc-avx2 blast/2.10.0+src
./blast/ncbi-blast-2.10.0+-src-gcc-sse4a blast/2.10.0+src
./blast/ncbi-blast-2.10.1+-src-gcc-avx512f blast/2.10.0+src
./blast/ncbi-blast-2.10.1+-src-gcc-sse4a blast/2.10.0+src
./blast/ncbi-blast-2.11.0+ blast/2.11.0+bin https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ 2.11.0+
./blast/refseq_genomic mod/version
./blat(35) blat/35 https://hgwdev.gi.ucsc.edu/~kent/exe/linux/ 36
./BLINK/0.01 mod/version https://github.com/Menggg/BLINK
./bowtie/bowtie-0.12.8 mod/version
./bowtie/bowtie-1.0.1 mod/version
./bowtie/bowtie-1.1.2 mod/version http://bowtie-bio.sourceforge.net/bowtie2/index.shtml 1.3.0
./bowtie2/bowtie2-2.1.0 mod/version
./bowtie2/bowtie2-2.2.0 mod/version
./bowtie2/bowtie2-2.2.3 mod/version
./bowtie2/bowtie2-2.2.8 mod/version
./bowtie2/bowtie2-2.2.9 mod/version
./bowtie2/bowtie2-2.3.3 mod/version
./bowtie2/bowtie2-2.3.3-binary mod/version
./bowtie2/bowtie2-2.3.4.1 mod/version
./bowtie2/bowtie2-2.3.5.1-sra-linux-x86_64 mod/version
./bowtie2/bowtie2-2.4.1-linux-x86_64 mod/version http://bowtie-bio.sourceforge.net/bowtie2/index.shtml 2.4.2
./busco/1.2.0 mod/version
./busco/3.0.1 busco/3.0.1
./busco/4.1.2 busco/4.1.2
./busco/busco-4.1.4 mod/version https://busco.ezlab.org/ 5.0.0
./bwa/bwa-0.7.9a mod/version
./bwa/bwa-0.7.10 mod/version
./bwa/bwa-0.7.17 mod/version https://sourceforge.net/projects/bio-bwa/files/ 0.7.17
./bwa-meth/0.2.2 python bioconda3-el7 bwameth.py https://github.com/brentp/bwa-meth/releases
./CAFE/4.2.1 CAFE/4.2.1 https://github.com/hahnlab/CAFE/releases/tag/v4.2.1 4.2.1
./canu/1.3 canu/1.3
./canu/1.7 canu/1.7
./canu/2.1 canu/2.1 https://github.com/marbl/canu/releases 2.1.1
./CAP3 mod/version http://seq.cs.iastate.edu/cap3.html ?
./cdhit/v4.6.5 mod/version
./cdhit/v4.6.8-2017-1208 mod/version https://github.com/weizhongli/cdhit 4.8.1
./Celera/(8.1) mod/version https://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/ 8.3
./clustalw/clustalw-2.1-linux-x86_64-libcppstatic mod/version http://www.clustal.org/download/current/ 2.1
./cnvnator(0.3.3) mod/version
./CNVnator(0.3.3) mod/version https://github.com/abyzovlab/CNVnator 0.4.1
./crb-blast/20151012 mod/version https://github.com/cboursnell/crb-blast deprecated
./CroCo/1.1(20180320) croco/1.1 https://github.com/cschmidtlab/croco 0.7
./cufflinks/cufflinks-2.2.1.Linux_x86_64 cufflinks/2.2.1
./cufflinks/cufflinks-2.2.2 mod/version https://github.com/cole-trapnell-lab/cufflinks/blob/master/README.md unknown
./cutadapt/cutadapt-1.41 cutadapt/1.4.1 https://cutadapt.readthedocs.io/en/stable/installation.html 3.2
./DataAnalysis/2.8_All mod/version 2.8
./datamash/1.0.5 mod/version
./datamash/1.3 mod/version https://ftp.gnu.org/gnu/datamash/ 1.7
./dDocent mod/version https://www.ddocent.com/downloads/ 2.7.8
./deepTools(2.2.4) mod/version https://github.com/deeptools/deepTools 3.5.0
./diamond/0.9.21.122 diamond/0.9.21.122
./diamond/2.0.1 diamond/2.0.1 https://github.com/bbuchfink/diamond 2.0.6
./dock/dock6 mod/version http://dock.compbio.ucsf.edu/DOCK_6/index.htm 6.9
./edirect/8.10 edirect/8.10 https://astrobiomike.github.io/unix/ncbi_eutils https://www.ncbi.nlm.nih.gov/books/NBK179288/
./eigen mod/version use_version_in_share
./emboss/6.6.0 mod/version
./emboss/6.6.0-gcc emboss/6.60 http://emboss.sourceforge.net/download/#Stable 6.6.0
./EnTAP(20180430) EnTAP/0.8.1 https://github.com/harta55/EnTAP/ 0.10.7
./epa-ng/0.3.6 epa-ng/0.3.6 https://github.com/Pbdas/epa-ng 0.3.8
./exonerate/2.2.0 mod/version
./exonerate/2.4.0 mod/version https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate 2.4.0
./eXpress/1.5.1 express/1.5.1 https://pachterlab.github.io/eXpress/overview.html
./falcon/FALCON-integrate-2016-05 mod/version https://github.com/PacificBiosciences/FALCON 0.3.0
./falcon/FALCON-integrate-2018-05 mod/version https://www.pacb.com/support/software-downloads/
./FALCON_unzip mod/version 1.2.0-deprecated
./fastANI/1.32 fastANI/1.32 https://github.com/ParBLiSS/FastANI 1.32
./fastqc/FastQC_v0.11.5 fastqc/0.11.5 ./bioinformatics/fastqc/FastQC_v0.11.9 https://www.bioinformatics.babraham.ac.uk/projects/download.html
./fastStructure(20170718) mod/version https://rajanil.github.io/fastStructure/ 1
./FastTree/test mod/version
./FastTree/2.1.10 mod/version http://www.microbesonline.org/fasttree/#Install 2.1.11
./fastx/fastx_toolkit-0.0.1 mod/version https://github.com/agordon/fastx_toolkit 0.0.14
./flash/FLASH-1.2.9 mod/version
./flash/FLASH-1.2.11 flash/1.2.11 http://ccb.jhu.edu/software/FLASH/index.shtml 1.2.11
./Flye(2.3.3) flye/2.3.3 https://github.com/fenderglass/Flye 2.8.2
./Flye/2.6 flye/2.6 https://github.com/fenderglass/Flye 2.8.2
./gappa/1.3.5 mod/version https://github.com/lczech/gappa 0.7.0
./GATK/GATK-3.5 mod/version
./GATK/4.0 gatk/4.0.0
./GATK/gatk-4.0.0.0 mod/version https://github.com/broadinstitute/gatk/releases 4.1.9.0
./GCTA/1.91.3beta mod/version https://cnsgenomics.com/software/gcta/#Download 1.93.2
./GCTA/build mod/version
./Gctf/v1.0.6 mod/version https://www2.mrc-lmb.cam.ac.uk/research/locally-developed-software/zhang-software/ 1.18
./gemma/0.94.1 gemma/0.94.1
./gemma/0.97 gemma/0.97 https://github.com/genetics-statistics/GEMMA 0.98.4
./genometools/1.5.8 genometools/1.5.8 https://github.com/genometools/genometools unknown
./guppy/2.3.7 mod/version
./guppy/3.2.2-cpu mod/version
./guppy/3.2.2-gpu mod/version
./guppy/3.2.4-cpu mod/version
./guppy/3.2.4-gpu mod/version
./guppy/4.0.11-gpu(20200708) guppy/4.0.11 login_Oxford_Nanopore
./guppy/4.4.1-gpu guppy/4.4.1
./guppy/4.4.1-nogpu guppy/4.4.1
./HipSTR/(0.6.1) mod/version https://github.com/tfwillems/HipSTR 0.7
./hisat2/hisat2-2.0.3-beta hisat2/2.0.3-beta
./hisat2/hisat2-2.1.0 hisat2/2.1.0
./hisat2/hisat2-2.2.1 hisat2/2.2.1 http://daehwankimlab.github.io/hisat2/ 2.2.1/beta-3N
./hmmer/3.1b2 mod/version
./hmmer/hmmer-3.1b2 mod/version
./hmmer/hmmer-3.1b2-intel-mvapich mod/version
./hmmer/hmmer-3.1b2-linux-intel-x86_64 mod/version http://hmmer.org/ 3.2
./htslib/1.1-pacbio mod/version
./htslib/1.3 mod/version
./htslib/1.7 mod/version
./htslib/1.10.2 mod/version http://www.htslib.org/download/ 1.11
./idba/1.1.3 mod/version https://github.com/loneknightpy/idba 1.1.3
./igb-5.3.5.4 mod/version https://bioviz.org/news.html 9.16
./IGV/IGV_Linux_2.8.0 mod/version https://software.broadinstitute.org/software/igv/download 2.9.0
./impute/impute_v2.3.2_x86_64_static mod/version https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#download 2.3.2
./infernal/1.1.1-gcc-impi infernal/1.1.1
./infernal/infernal-1.1.1-linux-intel-gcc infernal/1.1.1 http://eddylab.org/infernal/ 1.1.4
./iqtree/iqtree-omp-1.5.3-Linux mod/version
./iqtree/iqtree-1.6.9-Linux mod/version
./iqtree/iqtree-1.6.10-Linux mod/version
./iqtree/iqtree-1.6.12-Linux mod/version http://www.iqtree.org/ 1.6.12
./ISOWN isown/1.0 https://github.com/ikalatskaya/ISOWN release?
./jellyfish/2.2.6 jellyfish/2.2.6
./jellyfish/2.3.0 jellyfish/2.3.0 https://github.com/gmarcais/Jellyfish 2.3.0
./kallisto/kallisto_linux-v0.43.1 mod/version https://pachterlab.github.io/kallisto/download.html 0.46.1
./khmer/bz2file-0.98-py2.7.egg-info mod/version
./khmer/khmer-2.0-py2.7.egg-info mod/version https://github.com/dib-lab/khmer 2.1.2
./khmer/screed-0.9-py2.7.egg-info mod/version
./kmergenie/1.6476 mod/version http://kmergenie.bx.psu.edu/ 1.7051
./Ktrim/1.1.0 mod/version https://github.com/hellosunking/Ktrim 1.2.2.
./last/last-719 mod/version http://last.cbrc.jp/ last-1179
./lordec/lordec-src_0.9 mod/version https://gite.lirmm.fr/lordec/lordec-releases/-/wikis/home 0.9
./lorma/lorma-src_0.5a mod/version https://gite.lirmm.fr/lorma/lorma-releases/-/wikis/home 0.5
./lsc(1_alpha) mod/version https://web.stanford.edu/group/wonglab/LSC/LSC_download.html 1.alpha
./MACSE/v2.03 mod/version https://bioweb.supagro.inra.fr/macse/index.php?menu=releases 2.0.5
./mafft/7.304 mafft/7.304b https://mafft.cbrc.jp/alignment/software/ 7.475
./maker/maker maker/2.31.8
./maker/2.31.9b mod/version
./maker/maker-jpummil mod/version
./maker/2.31.9 maker/2.31.9 http://www.yandell-lab.org/software/maker.html 3.01.03
./MaSuRCA/3.4.2 MaSURCA/3.4.2 https://github.com/alekseyzimin/masurca 4.0.1
./mauve/2015-02-13 mod/version http://darlinglab.org/mauve/user-guide/versions.html 2.4.0
./mcl/12-135 mod/version
./mcl/14-137 mod/version https://micans.org/mcl/src/ 14-137
./megahit/v1.1.3 megahit/1.1.3 https://github.com/voutcn/megahit 1.2.9
./meme/meme_4.10.2 mod/version https://meme-suite.org/meme/doc/download.html 5.3.1
./meme/meme-4.10.2 mod/version
./MetaGeneMark/MetaGeneMark_linux_64 mod/version
./methyldactyl/0.5.1 methyldactyl/0.5.1 https://github.com/dpryan79/methyldackel
./migrate-n/migrate-3.6.6 mod/version https://peterbeerli.com/migrate-html5/download_version4/ 3.72/4.43
./metaphlan2/2.6.0 mod/version http://huttenhower.sph.harvard.edu/metaphlan 3
./miniasm miniasm/1.0
./minimap2 mod/version
./minimap2/minimap2-2.10_x64-linux minimap2/2.1
./minimap2/2.17 minimap2/2.17 https://github.com/lh3/minimap2 2.1.7
./mira/3.0.5 mod/version https://sourceforge.net/projects/mira-assembler/files/ 4.0.2
./miRDeep/mirdeep2_0_0_7 miRDeep/2.0.0.7
./miRDeep/mirdeep2_0_0_8 miRDeep/2.0.0.8 https://github.com/rajewsky-lab/mirdeep2 0.1.3
./modeller/9.14 mod/version https://salilab.org/modeller/download_installation.html 10
./mothur/mothur.1.25.0 mod/version
./mothur/mothur-1.35.1 mod/version
./mothur/mothur-1.36.1-intel-impi mod/version
./mothur/mothur-1.36.1-serial mod/version
./mothur/mothur-1.39.1 mod/version
./mothur/mothur-1.39.1-intel-impi mod/version
./mothur/mothur-1.39.1-serial mod/version
./mothur/mothur-1.39.5-serial mod/version
./mothur/mothur-1.40.5-serial mod/version
./mothur/1.44.2 mod/version https://github.com/mothur/mothur/releases/tag/v1.44.3
./mpiblast mod/version
./mrbayes/3.2.6-avx-openmp mrbayes/3.2.6
./mrbayes/3.2.6-avx-openmp-mpi mrbayes/3.2.6-mpi
./mrbayes/3.2.6-sse-openmp mrbayes/3.2.6
./mrbayes/3.2.6-sse-openmp-mpi mrbayes/3.2.6-mpi http://nbisweden.github.io/MrBayes/download.html 3.2.7a
./MultiQC/1.10.dev0 mod/version https://github.com/ewels/MultiQC 1.9
./MUMmer/MUMmer3.23 mod/version https://github.com/mummer4/mummer 4.0.0
./muscle/muscle3.8.31 muscle/3.8.31 http://www.drive5.com/muscle/downloads.htm 3.8.31
./mutect/1.1.7 mod/version https://software.broadinstitute.org/cancer/cga/mutect_download ?login
./MutMap/2.1.6 mod/version
./ncbi mod/version
./ncbi/ngs mod/version https://github.com/ncbi/ngs v?
./ncbi/share mod/version
./ncbi/sra-tools(2.7.0) sra-tools/2.7.0
./ncbi/sra-tools-2.8.1-3 sra-tools/2.8.1-3 https://github.com/ncbi/sra-tools/wiki/01.-Downloading-SRA-Toolkit 2.10.9
./ncbi/sra-toolkit.2.9.0 sra-tools/2.9.0
./newbler(unknown) mod/version
./newick-utils/1.6 newick-utils/1.61
./nextflow/20.10.0 nextflow/20.10.0
./nim/0.18.0 nim/0.18.0 https://nim-lang.org/install_unix.html 1.4.2
./ntedit mod/version
./oases/0.2.08 mod/version https://www.ebi.ac.uk/~zerbino/oases/ 0.2.08
./OrthoFinder/0.4.0 mod/version
./OrthoFinder/2.2.6 orthofinder/2.2.6
./OrthoFinder/2.4.0 mod/version
./OrthoFinder/2.4.0-tmpe mod/version https://github.com/davidemms/OrthoFinder 2.5.2
./orthomclSoftware/v2.0.9 mod/version
./PAML/paml4.6 PAML/4.6
./PAML/paml4.8 PAML/4.8
./PAML/paml4.9e PAML/4.9e http://abacus.gene.ucl.ac.uk/software/paml.html#download 4.9
./pandaseq mod/version https://github.com/neufeld/pandaseq 2.11(2017)
./Panseq mod/version https://github.com/chadlaing/Panseq 2017
./ParGenes mod/version https://github.com/BenoitMorel/ParGenes 1.2.0
./PASTA/1.8.2 mod/version
./PASTA/1.8.3 mod/version https://github.com/smirarab/pasta python
./pbcopper(2016) mod/version https://github.com/PacificBiosciences/pbcopper 1.9.0(2020)
./PBSuite/15.8.24 PBSuite/15.8.24 https://sourceforge.net/projects/pb-jelly/ 15.8.24
./pcit pcit/1.0
./pear/0.9.11 pear/0.9.11 https://github.com/tseemann/PEAR 0.9.11
./phylophlan mod/version
./phyx-incomplete mod/version https://github.com/FePhyFoFum/phyx 1.1(2020)
./picard/picard-tools-2.1.1 mod/version
./picard/picard-tools-2.17.10 mod/version https://github.com/broadinstitute/picard/releases/tag/2.24.2
./pilon/1.22 mod/version
./pindel mod/version https://github.com/genome/pindel 0.2.5b8(2015)
./pitchfork mod/version https://github.com/PacificBiosciences/pitchfork 2017
./plink/1.90b6.6 plink/1.90b6.6
./plink/1.90b6.10 plink/1.90b6.10 https://www.cog-genomics.org/plink2 1.90beta(20201019)
./plink/3.46 plink/3.46
./plink/5.2 plink/5.2 https://www.cog-genomics.org/plink/ 6.2.1
./pplacer/1.1-alpha19 pplacer/1.1-alpha19 https://github.com/matsen/pplacer
./prodigal/2.6.3 prodigal/2.6.3 https://github.com/hyattpd/Prodigal 2.6.3
./pysam/0.9.0 mod/version https://pypi.org/project/pysam/
./quast/quast-5.0.0 mod/version http://quast.sourceforge.net/install.html 5.0.2
./randfold/2.0.1 mod/version
./raven/1.1.0 mod/version https://github.com/SysBioChalmers/RAVEN 2.4.2
./RAxML/stamatak-standard-RAxML-5_7_2012 mod/version
./RAxML/RAXML-8.0.20 mod/version
./RAxML/RAxML-8.2.9 raxml/8.2.9 https://github.com/stamatak/standard-RAxML 8.2.12
./RAxML/RAxML-8.2.11 raxml/8.2.11 https://github.com/amkozlov/raxml-ng/releases 1.0.1
./Rcorrector(20160212) mod/version https://github.com/mourisl/Rcorrector 1.0.4(2019)
./rDock/2013.1 mod/version https://sourceforge.net/projects/rdock/files/?source=navbar 2013.1
./rdp_classifier/2.2 mod/version https://sourceforge.net/projects/rdp-classifier/ 2.13
./rdp_classifier/2.12 mod/version https://github.com/rdpstaff/classifier 2.10.2
./reapr/1.0.17 reapr/1.0.17 https://www.sanger.ac.uk/tool/reapr// 1.0.18
./RepeatMasker/4.0.7 RepeatMasker/4.0.7 http://www.repeatmasker.org/ 4.1.1
./root_digger/1.1.4 mod/version https://github.com/computations/root_digger 1.7.0
./rsem/1.2.27 mod/version
./rsem/1.3.0 mod/version
./rsem/1.3.3 mod/version http://deweylab.github.io/RSEM/ 1.3.3
./rsem/RSEM-1.3.3-install mod/version
./salmon/Salmon-0.8.2_linux_x86_64 salmon/0.8.2
./salmon/Salmon-0.14.1_linux_x86_64 salmon/0.14.1
./salmon/1.2.1 salmon/1.2.1
./salmon/1.4.0 salmon/1.4.0 https://github.com/COMBINE-lab/salmon 1.4.0
./sambamba/0.7.1 mod/version https://github.com/biod/sambamba 0.8.0
./samsa2 samsa/2.0 https://github.com/transcript/samsa2 2.2.0.1
./samstat/1.5.1 mod/version http://samstat.sourceforge.net/ 1.5.1
./samtools/1.3 mod/version
./samtools/1.4 mod/version
./samtools/1.7 mod/version
./samtools/1.9 mod/version
./samtools/1.10 mod/version
./samtools/bcftools-1.10.2 mod/version
./samtools/htslib-1.10.2 mod/version
./samtools/samtools-0.1.19 mod/version
./samtools/samtools-1.9 mod/version
./samtools/samtools-1.10 mod/version http://www.htslib.org/download/ 1.11
./sate-tools-linux/2018-04 mod/version https://github.com/sate-dev/sate-tools-linux 2013
./sepp/sepp-4.3.5 mod/version
./sepp/sepp-4.3.7 mod/version https://github.com/smirarab/sepp ?
./sepp-tools mod/version
./seqtk mod/version https://github.com/lh3/seqtk 1.3(2018)
./shapeit/extractPIRs mod/version
./shapeit/extractPIRs.v1.r68.x86_64 mod/version
./shapeit/shapeit.v2.904.2.6.32-696.18.7.el6.x86_64 mod/version
./shapeit/shapeit.v2.904.3.10.0-693.11.6.el7.x86_64 mod/version
./shapeit/r904 mod/version https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#download r904
./sickle/1.33 mod/version https://github.com/najoshi/sickle 1.33
./simple/1.8.1 mod/version https://github.com/wacguy/Simple-1.8.1 ?
./smrt/current smrt/6.0 https://www.pacb.com/support/software-downloads/ 9.0
./snap/2013-11-29 snap/2013-11-29 http://korflab.ucdavis.edu/software.html 2013-11-29
./snpEff mod/version https://pcingola.github.io/SnpEff/ 4.3T
./SOAPdenovo2/SOAPdenovo2-src-r240-gnu soapdenovo2/r240
./SOAPdenovo2/SOAPdenovo2-src-r240-intel soapdenovo2/r240 https://github.com/aquaskyline/SOAPdenovo2 242
./SOAPdenovo-Trans(2011) mod/version https://sourceforge.net/projects/soapdenovotrans/files/SOAPdenovo-Trans/ 1.0.3(2014)
./SomaticSniper mod/version http://gmt.genome.wustl.edu/packages/somatic-sniper/ 1.0.5.0
./sortmerna/2.1b mod/version https://bioinfo.lifl.fr/RNA/sortmerna/ 2.1
./spades/SPAdes-3.1.0 mod/version
./spades/SPAdes-3.5.0 mod/version
./spades/SPAdes-3.6.0 spades/3.12.0
./spades/SPAdes-3.8.1 mod/version
./spades/SPAdes-3.11.1 spades/3.12.0
./spades/SPAdes-3.12.0 spades/3.12.0
./spades/SPAdes-3.14.1 mod/version https://cab.spbu.ru/software/spades/ 3.15.0
./sra-tools/2.8.1-3 mod/version
./sratoolkit/2.6.2 mod/version
./sratoolkit/2.9.0 mod/version https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software 2.10.9
./sspace/3.0 mod/version https://github.com/nsoranzo/sspace_basic
./ssu-align/0.1.1 mod/version http://eddylab.org/software/ssu-align/ 0.1.1
./stacks/1.48 mod/version
./stacks/2.0B8C mod/version
./stacks/2.0B9 mod/version
./stacks/2.41 mod/version
./stacks/2.53 mod/version https://catchenlab.life.illinois.edu/stacks/ 2.55
./stampy/1.0.23 mod/version https://www.well.ox.ac.uk/research/scientific-cores/bioinformatics-statistical-genetics/software
./STAR/2.5 mod/version
./STAR/2.7.3a mod/version https://github.com/alexdobin/STAR 2.7.7a
./strelka/2 mod/version https://github.com/Illumina/strelka 2.9.10
./stringtie/stringtie-2.1.4.Linux_x86_64 mod/version http://www.ccb.jhu.edu/software/stringtie/ 2.1.4
./structure/2.3.4 mod/version https://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v2.3.4/html/structure.html 2.3.4
./subread/subread-2.0.1-Linux-x86_64 subread/2.0.1 http://subread.sourceforge.net/ 2.0.1
./swig/3.0.10 swig/3.0.10 http://www.swig.org/ 4.0.2
./tabix/0.2.5a mod/version
./tabix/0.2.5b mod/version Deprecated-see-samtools
./tassel/5-standalone tassel/5.0 https://bitbucket.org/tasseladmin/tassel-5-standalone/downloads/?tab=tags 5.2.69
./TopHat/2.1.1a mod/version
./TopHat/2.1.1b mod/version http://ccb.jhu.edu/software/tophat/index.shtml 2.11
./Tracer/v1.7.1 mod/version https://github.com/beast-dev/tracer/ 1.7.iii1
./transdecoder/5.5.0 transdecoder/5.5.0 https://github.com/TransDecoder/TransDecoder/releases 5.5.0
./trimal/1.4rev22 mod/version https://vicfero.github.io/trimal/index.html 2.0rev0
./trimmomatic/Trimmomatic-0.36 mod/version http://www.usadellab.org/cms/index.php?page=trimmomatic 0.39
./trinity/2.10.0 mod/version trinity/2.10.0
./trinity/trinityrnaseq-Trinity-v2.4.0 mod/version
./trinity/trinityrnaseq-v2.10.0
./trinity/trinityrnaseq-v2.11.0 trinity/group-2.11.0
./trinity/trinityrnaseq-v2.11.0 trinity/2.11.0 https://github.com/trinityrnaseq/trinityrnaseq/releases 2.11.0
./usearch/5.2.236 mod/version
./usearch/6.1.544 usearch/6.1
./usearch/8.0.1403 usearch/8.0
./usearch/8.1.1861 usearch/8.1
./usearch/10.0.240 mod/version https://www.drive5.com/usearch/download.html 11.0.667
./VarScan/2.3.9 mod/version https://github.com/dkoboldt/varscan 2.4.2
./vcftools/0.1.15 mod/version https://github.com/vcftools/vcftools 0.1.16
./velvet/velvet_1.2.10 mod/version https://www.ebi.ac.uk/~zerbino/velvet/ 1.2.10
./ViennaRNA ViennaRNA/2.2.8 https://www.tbi.univie.ac.at/RNA/#download 2.4.17
./vsearch/2.4.0 mod/version https://github.com/torognes/vsearch 2.15.2
./weka/3.8.2 mod/version https://sourceforge.net/projects/weka/files/ 3.8.5
./wgs/wgs-6.1 mod/version deprecated_see_Celera
./wise2/2.4.1 wise2/2.4.1 https://bioweb.pasteur.fr/packages/pack@wise2@2.4.1 2.4.1
./wombat/180404 mod/version http://didgeridoo.une.edu.au/km/wmbdownload1.php 25/02/20
bioinformatics_catalog.txt · Last modified: 2021/02/19 17:37 (external edit)

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