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bioinformatics_catalog

**This is an old revision of the document!**

Bioinformatics Software Catalog

Not including OpenHPC and other RPM software in /opt

/share/apps/bioinformatics_location Website latest_version
./abyss/abyss-1.3.7
./abyss/abyss-1.9.0
./abyss/2.0.2 https://www.bcgsc.ca/resources/software/abyss 2.1.5
./admixture/admixture_linux-1.3.0 https://bioinformaticshome.com/tools/descriptions/ADMIXTURE.html 1.3.0
./aegean/0.15.1 https://standage.github.io/AEGeAn/ 0.16.0
./allpaths-lg/51279 ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/ 52488
./annovar(20180416) https://annovar.openbioinformatics.org/en/latest/ 20210123
./astalavista/astalavista-3.2 http://sammeth.net/confluence/display/ASTA/Home
./ASTRAL(5.7.3) https://github.com/smirarab/ASTRAL 5.7.3
./augustus/3.22 http://bioinf.uni-greifswald.de/augustus/ 3.4.9
./b2g4pipe(2.5) https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/b2g4pipe-2-5 2.5
./BA3-SNPS-autotune(20200825) https://github.com/stevemussmann/BA3-SNPS-autotune 2.1.2
./bam2fastq/1.1.0 https://gslweb.discoveryls.com/information/software/bam2fastq 1.1.0
./bamtools/2.4.1 https://github.com/pezmaster31/bamtools 2.5.1
./BayesAss3-SNPs https://github.com/stevemussmann/BayesAss3-SNPs 1.1
./bbmap/34.30
./bbmap/38.79
./bbmap/38.82 https://sourceforge.net/projects/bbmap/ 38.9
./bcftools/1.10.2 https://github.com/samtools/bcftools 1.11
./beagle/2.1.2
./beagle/2.4.2
./beagle/2.4.2-avx-openmp
./beagle/2.4.2-sse-openmp https://faculty.washington.edu/browning/beagle/beagle.html 5.1
./beast/2.4
./beast/beast2.4.7 https://www.beast2.org/ 2.6
./bedtools2/2.25.0 https://bedtools.readthedocs.io/en/latest/ 2.28
./bfc https://github.com/lh3/bfc -2014
./bismark/0.23.0 https://github.com/FelixKrueger/Bismark 0.23.0
./blasr/5.3 https://github.com/PacificBiosciences/blasr 5.3.3
./blast/blast-2.2.22
./blast/db20150912
./blast/ncbi-blast-2.2.29+
./blast/ncbi-blast-2.3.0+
./blast/ncbi-blast-2.4.0+
./blast/ncbi-blast-2.5.0+
./blast/ncbi-blast-2.6.0+
./blast/ncbi-blast-2.6.0+-src
./blast/ncbi-blast-2.7.1+
./blast/ncbi-blast-2.9.0+
./blast/ncbi-blast-2.9.0+-src-gcc-sse4a
./blast/ncbi-blast-2.10.0+
./blast/ncbi-blast-2.10.0+-src-gcc-avx
./blast/ncbi-blast-2.10.0+-src-gcc-avx2
./blast/ncbi-blast-2.10.0+-src-gcc-sse4a
./blast/ncbi-blast-2.10.1+-src-gcc-avx512f
./blast/ncbi-blast-2.10.1+-src-gcc-sse4a
./blast/ncbi-blast-2.11.0+ https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ 2.11.0+
./blast/refseq_genomic
./blat(35) https://hgwdev.gi.ucsc.edu/~kent/exe/linux/ 36
./BLINK/0.01 https://github.com/Menggg/BLINK
./bowtie/bowtie-0.12.8
./bowtie/bowtie-1.0.1
./bowtie/bowtie-1.1.2 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml 1.3.0
./bowtie2/bowtie2-2.1.0
./bowtie2/bowtie2-2.2.0
./bowtie2/bowtie2-2.2.3
./bowtie2/bowtie2-2.2.8
./bowtie2/bowtie2-2.2.9
./bowtie2/bowtie2-2.3.3
./bowtie2/bowtie2-2.3.3-binary
./bowtie2/bowtie2-2.3.4.1
./bowtie2/bowtie2-2.3.5.1-sra-linux-x86_64
./bowtie2/bowtie2-2.4.1-linux-x86_64 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml 2.4.2
./busco/1.2.0
./busco/3.0.1
./busco/4.1.2
./busco/busco-4.1.4 https://busco.ezlab.org/ 5.0.0
./bwa/bwa-0.7.9a
./bwa/bwa-0.7.10
./bwa/bwa-0.7.17 https://sourceforge.net/projects/bio-bwa/files/ 0.7.17
./CAFE/4.2.1 https://github.com/hahnlab/CAFE/releases/tag/v4.2.1 4.2.1
./canu/1.3
./canu/1.7
./canu/2.1 https://github.com/marbl/canu/releases 2.1.1
./CAP3 http://seq.cs.iastate.edu/cap3.html ?
./cdhit/v4.6.5
./cdhit/v4.6.8-2017-1208 https://github.com/weizhongli/cdhit 4.8.1
./Celera/(8.1) https://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/ 8.3
./clustalw/clustalw-2.1-linux-x86_64-libcppstatic http://www.clustal.org/download/current/ 2.1
./cnvnator(0.3.3)
./CNVnator(0.3.3) https://github.com/abyzovlab/CNVnator 0.4.1
./crb-blast/20151012 https://github.com/cboursnell/crb-blast deprecated
./CroCo/1.1(20180320) https://github.com/cschmidtlab/croco 0.7
./cufflinks/cufflinks-2.2.1.Linux_x86_64
./cufflinks/cufflinks-2.2.2 https://github.com/cole-trapnell-lab/cufflinks/blob/master/README.md unknown
./cutadapt/cutadapt-1.41 https://cutadapt.readthedocs.io/en/stable/installation.html 3.2
./DataAnalysis/2.8_All 2.8
./datamash/1.0.5
./datamash/1.3 https://ftp.gnu.org/gnu/datamash/ 1.7
./dDocent https://www.ddocent.com/downloads/ 2.7.8
./deepTools(2.2.4) https://github.com/deeptools/deepTools 3.5.0
./diamond/0.9.21.122
./diamond/2.0.1 https://github.com/bbuchfink/diamond 2.0.6
./dock/dock6 http://dock.compbio.ucsf.edu/DOCK_6/index.htm 6.9
./edirect/8.10 https://astrobiomike.github.io/unix/ncbi_eutils , https://www.ncbi.nlm.nih.gov/books/NBK179288/
./eigen use_version_in_share
./emboss/6.6.0
./emboss/6.6.0-gcc http://emboss.sourceforge.net/download/#Stable 6.6.0
./EnTAP(20180430) https://github.com/harta55/EnTAP/ 0.10.7
./epa-ng/0.3.6 https://github.com/Pbdas/epa-ng 0.3.8
./exonerate/2.2.0
./exonerate/2.4.0 https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate 2.4.0
./falcon/FALCON-integrate-2016-05 https://github.com/PacificBiosciences/FALCON 0.3.0
./falcon/FALCON-integrate-2018-05 https://www.pacb.com/support/software-downloads/
./FALCON_unzip 1.2.0-deprecated
./fastqc/FastQC_v0.11.5 ./bioinformatics/fastqc/FastQC_v0.11.9 , https://www.bioinformatics.babraham.ac.uk/projects/download.html
./fastStructure(20170718) https://rajanil.github.io/fastStructure/ 1
./FastTree/test
./FastTree/2.1.10 http://www.microbesonline.org/fasttree/#Install 2.1.11
./fastx/fastx_toolkit-0.0.1 https://github.com/agordon/fastx_toolkit 0.0.14
./flash/FLASH-1.2.9
./flash/FLASH-1.2.11 http://ccb.jhu.edu/software/FLASH/index.shtml 1.2.11
./Flye/2.6 https://github.com/fenderglass/Flye 2.8.2
./gappa/1.3.5 https://github.com/lczech/gappa 0.7.0
./GATK/GATK-3.5
./GATK/4.0
./GATK/gatk-4.0.0.0 https://github.com/broadinstitute/gatk/releases 4.1.9.0
./GCTA/1.91.3beta https://cnsgenomics.com/software/gcta/#Download 1.93.2
./GCTA/build
./Gctf/v1.0.6 https://www2.mrc-lmb.cam.ac.uk/research/locally-developed-software/zhang-software/ 1.18
./gemma/0.94.1
./gemma/0.97 https://github.com/genetics-statistics/GEMMA 0.98.4
./genometools/1.5.8 https://github.com/genometools/genometools unknown
./guppy/2.3.7
./guppy/3.2.2-cpu
./guppy/3.2.2-gpu
./guppy/3.2.4-cpu
./guppy/3.2.4-gpu
./guppy/4.0.11-gpu(20200708) login_Oxford_Nanopore
./HipSTR/(0.6.1) https://github.com/tfwillems/HipSTR 0.7
./hisat2/hisat2-2.0.3-beta
./hisat2/hisat2-2.1.0
./hisat2/hisat2-2.2.1 http://daehwankimlab.github.io/hisat2/ 2.2.1/beta-3N
./hmmer/3.1b2
./hmmer/hmmer-3.1b2
./hmmer/hmmer-3.1b2-intel-mvapich
./hmmer/hmmer-3.1b2-linux-intel-x86_64 http://hmmer.org/ 3.2
./htslib/1.1-pacbio
./htslib/1.3
./htslib/1.7
./htslib/1.10.2 http://www.htslib.org/download/ 1.11
./idba/1.1.3 https://github.com/loneknightpy/idba 1.1.3
./IGV/IGV_Linux_2.8.0 https://software.broadinstitute.org/software/igv/download 2.9.0
./impute/impute_v2.3.2_x86_64_static https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#download 2.3.2
./infernal/1.1.1-gcc-impi
./infernal/infernal-1.1.1-linux-intel-gcc http://eddylab.org/infernal/ 1.1.4
./iqtree/iqtree-omp-1.5.3-Linux
./iqtree/iqtree-1.6.9-Linux
./iqtree/iqtree-1.6.10-Linux
./iqtree/iqtree-1.6.12-Linux http://www.iqtree.org/ 1.6.12
./ISOWN https://github.com/ikalatskaya/ISOWN release?
./jellyfish/2.2.6
./jellyfish/2.3.0 https://github.com/gmarcais/Jellyfish 2.3.0
./kallisto/kallisto_linux-v0.43.1 https://pachterlab.github.io/kallisto/download.html 0.46.1
./khmer/bz2file-0.98-py2.7.egg-info
./khmer/khmer-2.0-py2.7.egg-info https://github.com/dib-lab/khmer 2.1.2
./khmer/screed-0.9-py2.7.egg-info
./kmergenie/1.6476 http://kmergenie.bx.psu.edu/ 1.7051
./Ktrim/1.1.0 https://github.com/hellosunking/Ktrim 1.2.2.
./last/last-719 http://last.cbrc.jp/ last-1179
./lordec/lordec-src_0.9 https://gite.lirmm.fr/lordec/lordec-releases/-/wikis/home 0.9
./lorma/lorma-src_0.5a https://gite.lirmm.fr/lorma/lorma-releases/-/wikis/home 0.5
./lsc(1_alpha) https://web.stanford.edu/group/wonglab/LSC/LSC_download.html 1.alpha
./MACSE/v2.03 https://bioweb.supagro.inra.fr/macse/index.php?menu=releases 2.0.5
./mafft/7.304 https://mafft.cbrc.jp/alignment/software/ 7.475
./maker/2.31.9
./maker/2.31.9b
./maker/maker
./maker/maker-jpummil http://www.yandell-lab.org/software/maker.html 3.01.03
./MaSuRCA/3.4.2 https://github.com/alekseyzimin/masurca 4.0.1
./mauve/2015-02-13 http://darlinglab.org/mauve/user-guide/versions.html 2.4.0
./mcl/12-135
./mcl/14-137 https://micans.org/mcl/src/ 14-137
./megahit/v1.1.3 https://github.com/voutcn/megahit 1.2.9
./meme/meme_4.10.2 https://meme-suite.org/meme/doc/download.html 5.3.1
./meme/meme-4.10.2
./MetaGeneMark/MetaGeneMark_linux_64
./metaphlan2/2.6.0 http://huttenhower.sph.harvard.edu/metaphlan 3
./miniasm
./minimap2
./minimap2/minimap2-2.10_x64-linux
./minimap2/2.17 https://github.com/lh3/minimap2 2.1.7
./mira/3.0.5 https://sourceforge.net/projects/mira-assembler/files/ 4.0.2
./miRDeep/mirdeep2_0_0_7
./miRDeep/mirdeep2_0_0_8 https://github.com/rajewsky-lab/mirdeep2 0.1.3
./modeller/9.14 https://salilab.org/modeller/download_installation.html 10
./mothur/mothur.1.25.0
./mothur/mothur-1.35.1
./mothur/mothur-1.36.1-intel-impi
./mothur/mothur-1.36.1-serial
./mothur/mothur-1.39.1
./mothur/mothur-1.39.1-intel-impi
./mothur/mothur-1.39.1-serial
../mothur/mothur-1.39.5-serial
../mothur/mothur-1.40.5-serial
./mothur/1.44.2 https://github.com/mothur/mothur/releases/tag/v1.44.3
./mpiblast
./mrbayes/3.2.6-avx-openmp
./mrbayes/3.2.6-avx-openmp-mpi
./mrbayes/3.2.6-sse-openmp
./mrbayes/3.2.6-sse-openmp-mpi http://nbisweden.github.io/MrBayes/download.html 3.2.7a
./MultiQC/1.10.dev0 https://github.com/ewels/MultiQC 1.9
./MUMmer/MUMmer3.23 https://github.com/mummer4/mummer 4.0.0
./muscle/muscle3.8.31 http://www.drive5.com/muscle/downloads.htm 3.8.31
./mutect/1.1.7 https://software.broadinstitute.org/cancer/cga/mutect_download ?login
./MutMap/2.1.6
./ncbi
./ncbi/ngs https://github.com/ncbi/ngs v?
./ncbi/share
./ncbi/sra-tools
./ncbi/sra-tools-2.8.1-3 https://github.com/ncbi/sra-tools/wiki/01.-Downloading-SRA-Toolkit 2.10.9
./newbler(unknown)
./newick-utils/1.6
./nextflow/20.10.0
./nim/0.18.0 https://nim-lang.org/install_unix.html 1.4.2
./ntedit
./oases/0.2.08 https://www.ebi.ac.uk/~zerbino/oases/ 0.2.08
./OrthoFinder/0.4.0
./OrthoFinder/2.2.6
./OrthoFinder/2.4.0
./OrthoFinder/2.4.0-tmpe https://github.com/davidemms/OrthoFinder 2.5.2
./orthomclSoftware/v2.0.9
./PAML/paml4.6
./PAML/paml4.8
./PAML/paml4.9e http://abacus.gene.ucl.ac.uk/software/paml.html#download 4.9
./pandaseq https://github.com/neufeld/pandaseq 2.11(2017)
./Panseq https://github.com/chadlaing/Panseq 2017
./ParGenes https://github.com/BenoitMorel/ParGenes 1.2.0
./PASTA/1.8.2
./PASTA/1.8.3 https://github.com/smirarab/pasta python
./pbcopper(2016) https://github.com/PacificBiosciences/pbcopper 1.9.0(2020)
./PBSuite/15.8.24 https://sourceforge.net/projects/pb-jelly/ 15.8.24
./pcit
./pear/0.9.11 https://github.com/tseemann/PEAR 0.9.11
./phylophlan
./phyx-incomplete https://github.com/FePhyFoFum/phyx 1.1(2020)
./picard/picard-tools-2.1.1
./picard/picard-tools-2.17.10 https://github.com/broadinstitute/picard/releases/tag/2.24.2
./pilon/1.22
./pindel https://github.com/genome/pindel 0.2.5b8(2015)
./pitchfork https://github.com/PacificBiosciences/pitchfork 2017
./plink/1.90b6.6
./plink/1.90b6.10 https://www.cog-genomics.org/plink2 1.90beta(20201019)
./plink/3.46
./plink/5.2 https://www.cog-genomics.org/plink/ 6.2.1
./pysam/0.9.0 https://pypi.org/project/pysam/
./quast/quast-5.0.0 http://quast.sourceforge.net/install.html 5.0.2
./randfold/2.0.1
./raven/1.1.0 https://github.com/SysBioChalmers/RAVEN 2.4.2
./RAxML/stamatak-standard-RAxML-5_7_2012
./RAxML/RAXML-8.0.20
./RAxML/RAxML-8.2.9 https://github.com/stamatak/standard-RAxML 8.2.12
./RAxML/RAxML-8.2.11 https://github.com/amkozlov/raxml-ng/releases 1.0.1
./Rcorrector(20160212) https://github.com/mourisl/Rcorrector 1.0.4(2019)
./rDock/2013.1 https://sourceforge.net/projects/rdock/files/?source=navbar 2013.1
./rdp_classifier/2.2 https://sourceforge.net/projects/rdp-classifier/ 2.13
./rdp_classifier/2.12 https://github.com/rdpstaff/classifier 2.10.2
./reapr/1.0.17 https://www.sanger.ac.uk/tool/reapr// 1.0.18
./RepeatMasker/4.0.7 http://www.repeatmasker.org/ 4.1.1
./root_digger/1.1.4 https://github.com/computations/root_digger 1.7.0
./rsem/1.2.27
./rsem/1.3.0
./rsem/1.3.3 http://deweylab.github.io/RSEM/ 1.3.3
./rsem/RSEM-1.3.3-install
./salmon/Salmon-0.8.2_linux_x86_64
./salmon/Salmon-0.14.1_linux_x86_64
./salmon/1.2.1
./salmon/1.2.1-install https://github.com/COMBINE-lab/salmon 1.4.0
./sambamba/0.7.1 https://github.com/biod/sambamba 0.8.0
./samsa2 https://github.com/transcript/samsa2 2.2.0.1
./samstat/1.5.1 http://samstat.sourceforge.net/ 1.5.1
./samtools/1.3
./samtools/1.4
./samtools/1.7
./samtools/1.9
./samtools/1.10
./samtools/bcftools-1.10.2
./samtools/htslib-1.10.2
./samtools/samtools-0.1.19
./samtools/samtools-1.9
./samtools/samtools-1.10 http://www.htslib.org/download/ 1.11
./sate-tools-linux/2018-04 https://github.com/sate-dev/sate-tools-linux 2013
./sepp/sepp-4.3.5
./sepp/sepp-4.3.7 https://github.com/smirarab/sepp ?
./sepp-tools
./seqtk https://github.com/lh3/seqtk 1.3(2018)
./shapeit/extractPIRs
./shapeit/extractPIRs.v1.r68.x86_64
./shapeit/shapeit.v2.904.2.6.32-696.18.7.el6.x86_64
./shapeit/shapeit.v2.904.3.10.0-693.11.6.el7.x86_64
./shapeit/r904 https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#download r904
./sickle/1.33 https://github.com/najoshi/sickle 1.33
./simple/1.8.1 https://github.com/wacguy/Simple-1.8.1 ?
./smrtlink https://www.pacb.com/support/software-downloads/ 9
./snap/2013-11-29 http://korflab.ucdavis.edu/software.html 2013-11-29
./snpEff https://pcingola.github.io/SnpEff/ 4.3T
./SOAPdenovo2/SOAPdenovo2-src-r240-gnu
./SOAPdenovo2/SOAPdenovo2-src-r240-intel https://github.com/aquaskyline/SOAPdenovo2 242
./SOAPdenovo-Trans(2011) https://sourceforge.net/projects/soapdenovotrans/files/SOAPdenovo-Trans/ 1.0.3(2014)
./SomaticSniper http://gmt.genome.wustl.edu/packages/somatic-sniper/ 1.0.5.0
./sortmerna/2.1b https://bioinfo.lifl.fr/RNA/sortmerna/ 2.1
./spades/SPAdes-3.1.0
./spades/SPAdes-3.5.0
./spades/SPAdes-3.6.0
./spades/SPAdes-3.8.1
./spades/SPAdes-3.11.1
./spades/SPAdes-3.12.0
./spades/SPAdes-3.14.1 https://cab.spbu.ru/software/spades/ 3.15.0
./sra-tools/2.8.1-3
./sratoolkit/2.6.2
./sratoolkit/2.9.0 https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software 2.10.9
./sspace/3.0 https://github.com/nsoranzo/sspace_basic
./ssu-align/0.1.1 http://eddylab.org/software/ssu-align/ 0.1.1
./stacks/1.48
./stacks/2.0B8C
./stacks/2.0B9
./stacks/2.41
./stacks/2.53 https://catchenlab.life.illinois.edu/stacks/ 2.55
./stampy/1.0.23 https://www.well.ox.ac.uk/research/scientific-cores/bioinformatics-statistical-genetics/software
./STAR/2.5
./STAR/2.7.3a https://github.com/alexdobin/STAR 2.7.7a
./strelka/2 https://github.com/Illumina/strelka 2.9.10
./stringtie/stringtie-2.1.4.Linux_x86_64 http://www.ccb.jhu.edu/software/stringtie/ 2.1.4
./structure/2.3.4 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 http://subread.sourceforge.net/ 2.0.1
./swig/3.0.10 http://www.swig.org/ 4.0.2
./tabix/0.2.5a
./tabix/0.2.5b Deprecated-see-samtools
./tassel/5-standalone https://bitbucket.org/tasseladmin/tassel-5-standalone/downloads/?tab=tags 5.2.69
./TopHat/2.1.1a
./TopHat/2.1.1b http://ccb.jhu.edu/software/tophat/index.shtml 2.11
./Tracer/v1.7.1 https://github.com/beast-dev/tracer/ 1.7.iii1
./transdecoder/5.5.0 https://github.com/TransDecoder/TransDecoder/releases 5.5.0
./trimal/1.4rev22 https://vicfero.github.io/trimal/index.html 2.0rev0
./trimmomatic/Trimmomatic-0.36 http://www.usadellab.org/cms/index.php?page=trimmomatic 0.39
./trinity/2.10.0
./trinity/trinityrnaseq-Trinity-v2.4.0
./trinity/trinityrnaseq-v2.10.0
./trinity/trinityrnaseq-v2.11.0 https://github.com/trinityrnaseq/trinityrnaseq/releases 2.11.0
./usearch/5.2.236
./usearch/6.1.544
./usearch/8.0.1403
./usearch/8.1.1861
./usearch/10.0.240 https://www.drive5.com/usearch/download.html 11.0.667
./VarScan/2.3.9 https://github.com/dkoboldt/varscan 2.4.2
./vcftools/0.1.15 https://github.com/vcftools/vcftools 0.1.16
./velvet/velvet_1.2.10 https://www.ebi.ac.uk/~zerbino/velvet/ 1.2.10
./ViennaRNA https://www.tbi.univie.ac.at/RNA/#download 2.4.17
./vsearch/2.4.0 https://github.com/torognes/vsearch 2.15.2
./weka/3.8.2 https://sourceforge.net/projects/weka/files/ 3.8.5
./wgs/wgs-6.1 deprecated_see_Celera
./wombat/180404 http://didgeridoo.une.edu.au/km/wmbdownload1.php 25/02/20
bioinformatics_catalog.1612806678.txt.gz · Last modified: 2021/02/08 17:51 by root

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