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 |