| |
| bioinformatics_catalog [2021/02/08 17:51] – created root | bioinformatics_catalog [2025/10/15 19:51] (current) – external edit 127.0.0.1 |
|---|
| ===== Bioinformatics Software Catalog ===== | ===== Bioinformatics Software Catalog ===== |
| Not including OpenHPC and other RPM software in /opt | Not including OpenHPC and other RPM software in /opt and R/python/perl modules |
| <csv> | <csv> |
| /share/apps/bioinformatics_location , Website , latest_version | /share/apps/bioinformatics_Location , mod/version , Website latest_version |
| ./abyss/abyss-1.3.7 , , | ./abyss/abyss-1.3.7 , mod/version , |
| ./abyss/abyss-1.9.0 , , | ./abyss/abyss-1.9.0 , mod/version , |
| ./abyss/2.0.2 , https://www.bcgsc.ca/resources/software/abyss , 2.1.5 | ./abyss/2.0.2 , mod/version , 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 | ./admixture/admixture_linux-1.3.0 , mod/version , https://bioinformaticshome.com/tools/descriptions/ADMIXTURE.html 1.3.0 |
| ./aegean/0.15.1 , https://standage.github.io/AEGeAn/ , 0.16.0 | ./aegean/0.15.1 , mod/version , https://standage.github.io/AEGeAn/ 0.16.0 |
| ./allpaths-lg/51279 , ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/ , 52488 | ./allpaths-lg/51279 , mod/version , ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/ 52488 |
| ./annovar(20180416) , https://annovar.openbioinformatics.org/en/latest/ , 20210123 | ./annovar(20180416) , annovar/1.0 , https://annovar.openbioinformatics.org/en/latest/ 20210123 |
| ./astalavista/astalavista-3.2 , http://sammeth.net/confluence/display/ASTA/Home , | ./astalavista/astalavista-3.2 , mod/version , http://sammeth.net/confluence/display/ASTA/Home |
| ./ASTRAL(5.7.3) , https://github.com/smirarab/ASTRAL , 5.7.3 | ./ASTRAL(5.7.3) , mod/version , https://github.com/smirarab/ASTRAL 5.7.3 |
| ./augustus/3.22 , http://bioinf.uni-greifswald.de/augustus/ , 3.4.9 | ./augustus/3.22 , augustus/3.2.2 , 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 | ./b2g4pipe(2.5) , mod/version , 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 | ./BA3-SNPS-autotune(20200825) , mod/version , https://github.com/stevemussmann/BA3-SNPS-autotune 2.1.2 |
| ./bam2fastq/1.1.0 , https://gslweb.discoveryls.com/information/software/bam2fastq , 1.1.0 | ./bam2fastq/1.1.0 , mod/version , https://gslweb.discoveryls.com/information/software/bam2fastq 1.1.0 |
| ./bamtools/2.4.1 , https://github.com/pezmaster31/bamtools , 2.5.1 | ./bamtools/2.4.1 , mod/version , https://github.com/pezmaster31/bamtools 2.5.1 |
| ./BayesAss3-SNPs , https://github.com/stevemussmann/BayesAss3-SNPs , 1.1 | ./BayesAss3-SNPs , mod/version , https://github.com/stevemussmann/BayesAss3-SNPs 1.1 |
| ./bbmap/34.30 , , | ./bbmap/34.30 , bbmap/34.30 , |
| ./bbmap/38.79 , , | ./bbmap/38.79 , bbmap/38.79 , |
| ./bbmap/38.82 , https://sourceforge.net/projects/bbmap/ , 38.9 | ./bbmap/38.82 , bbmap/38.82 , https://sourceforge.net/projects/bbmap/ 38.9 |
| ./bcftools/1.10.2 , https://github.com/samtools/bcftools , 1.11 | ./bcftools/1.10.2 , mod/version , https://github.com/samtools/bcftools 1.11 |
| ./beagle/2.1.2 , , | ./beagle/2.1.2 , mod/version , |
| ./beagle/2.4.2 , , | ./beagle/2.4.2 , mod/version , |
| ./beagle/2.4.2-avx-openmp , , | ./beagle/2.4.2-avx-openmp , mod/version , |
| ./beagle/2.4.2-sse-openmp , https://faculty.washington.edu/browning/beagle/beagle.html , 5.1 | ./beagle/2.4.2-sse-openmp , mod/version , https://faculty.washington.edu/browning/beagle/beagle.html 5.1 |
| ./beast/2.4 , , | ./beast/2.4 , mod/version , |
| ./beast/beast2.4.7 , https://www.beast2.org/ , 2.6 | ./beast/beast2.4.7 , mod/version , https://www.beast2.org/ 2.6 |
| ./bedtools2/2.25.0 , https://bedtools.readthedocs.io/en/latest/ , 2.28 | ./bedtools2/2.25.0 , mod/version , https://bedtools.readthedocs.io/en/latest/ 2.28 |
| ./bfc , https://github.com/lh3/bfc , -2014 | ./bfc , mod/version , https://github.com/lh3/bfc -2014 |
| ./bismark/0.23.0 , https://github.com/FelixKrueger/Bismark , 0.23.0 | ./bismark/0.23.0 , mod/version , https://github.com/FelixKrueger/Bismark 0.23.0 |
| ./blasr/5.3 , https://github.com/PacificBiosciences/blasr , 5.3.3 | ./blasr/5.3 , blasr/5.3 , https://github.com/PacificBiosciences/blasr 5.3.3 |
| ./blast/blast-2.2.22 , , | ./blast/blast-2.2.22 , mod/version , |
| ./blast/db20150912 , , | ./blast/db20150912 , mod/version , |
| ./blast/ncbi-blast-2.2.29+ , , | ./blast/ncbi-blast-2.2.29+ , mod/version , |
| ./blast/ncbi-blast-2.3.0+ , , | ./blast/ncbi-blast-2.3.0+ , mod/version , |
| ./blast/ncbi-blast-2.4.0+ , , | ./blast/ncbi-blast-2.4.0+ , mod/version , |
| ./blast/ncbi-blast-2.5.0+ , , | ./blast/ncbi-blast-2.5.0+ , mod/version , |
| ./blast/ncbi-blast-2.6.0+ , , | ./blast/ncbi-blast-2.6.0+ , mod/version , |
| ./blast/ncbi-blast-2.6.0+-src , , | ./blast/ncbi-blast-2.6.0+-src , mod/version , |
| ./blast/ncbi-blast-2.7.1+ , , | ./blast/ncbi-blast-2.7.1+ , mod/version , |
| ./blast/ncbi-blast-2.9.0+ , , | ./blast/ncbi-blast-2.9.0+ , blast/2.9.0+ , |
| ./blast/ncbi-blast-2.9.0+-src-gcc-sse4a , , | ./blast/ncbi-blast-2.9.0+-src-gcc-sse4a , mod/version , |
| ./blast/ncbi-blast-2.10.0+ , , | ./blast/ncbi-blast-2.10.0+ , blast/2.10.0+bin , |
| ./blast/ncbi-blast-2.10.0+-src-gcc-avx , , | ./blast/ncbi-blast-2.10.0+-src-gcc-avx , blast/2.10.0+src , |
| ./blast/ncbi-blast-2.10.0+-src-gcc-avx2 , , | ./blast/ncbi-blast-2.10.0+-src-gcc-avx2 , blast/2.10.0+src , |
| ./blast/ncbi-blast-2.10.0+-src-gcc-sse4a , , | ./blast/ncbi-blast-2.10.0+-src-gcc-sse4a , blast/2.10.0+src , |
| ./blast/ncbi-blast-2.10.1+-src-gcc-avx512f , , | ./blast/ncbi-blast-2.10.1+-src-gcc-avx512f , blast/2.10.0+src , |
| ./blast/ncbi-blast-2.10.1+-src-gcc-sse4a , , | ./blast/ncbi-blast-2.10.1+-src-gcc-sse4a , blast/2.10.0+src , |
| ./blast/ncbi-blast-2.11.0+ , https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ , 2.11.0+ | ./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 , , | ./blast/refseq_genomic , mod/version , |
| ./blat(35) , https://hgwdev.gi.ucsc.edu/~kent/exe/linux/ , 36 | ./blat(35) , blat/35 , https://hgwdev.gi.ucsc.edu/~kent/exe/linux/ 36 |
| ./BLINK/0.01 , https://github.com/Menggg/BLINK , | ./BLINK/0.01 , mod/version , https://github.com/Menggg/BLINK |
| ./bowtie/bowtie-0.12.8 , , | ./bowtie/bowtie-0.12.8 , mod/version , |
| ./bowtie/bowtie-1.0.1 , , | ./bowtie/bowtie-1.0.1 , mod/version , |
| ./bowtie/bowtie-1.1.2 , http://bowtie-bio.sourceforge.net/bowtie2/index.shtml , 1.3.0 | ./bowtie/bowtie-1.1.2 , mod/version , http://bowtie-bio.sourceforge.net/bowtie2/index.shtml 1.3.0 |
| ./bowtie2/bowtie2-2.1.0 , , | ./bowtie2/bowtie2-2.1.0 , mod/version , |
| ./bowtie2/bowtie2-2.2.0 , , | ./bowtie2/bowtie2-2.2.0 , mod/version , |
| ./bowtie2/bowtie2-2.2.3 , , | ./bowtie2/bowtie2-2.2.3 , mod/version , |
| ./bowtie2/bowtie2-2.2.8 , , | ./bowtie2/bowtie2-2.2.8 , mod/version , |
| ./bowtie2/bowtie2-2.2.9 , , | ./bowtie2/bowtie2-2.2.9 , mod/version , |
| ./bowtie2/bowtie2-2.3.3 , , | ./bowtie2/bowtie2-2.3.3 , mod/version , |
| ./bowtie2/bowtie2-2.3.3-binary , , | ./bowtie2/bowtie2-2.3.3-binary , mod/version , |
| ./bowtie2/bowtie2-2.3.4.1 , , | ./bowtie2/bowtie2-2.3.4.1 , mod/version , |
| ./bowtie2/bowtie2-2.3.5.1-sra-linux-x86_64 , , | ./bowtie2/bowtie2-2.3.5.1-sra-linux-x86_64 , mod/version , |
| ./bowtie2/bowtie2-2.4.1-linux-x86_64 , http://bowtie-bio.sourceforge.net/bowtie2/index.shtml , 2.4.2 | ./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 , , | ./busco/1.2.0 , mod/version , |
| ./busco/3.0.1 , , | ./busco/3.0.1 , busco/3.0.1 , |
| ./busco/4.1.2 , , | ./busco/4.1.2 , busco/4.1.2 , |
| ./busco/busco-4.1.4 , https://busco.ezlab.org/ , 5.0.0 | ./busco/busco-4.1.4 , mod/version , https://busco.ezlab.org/ 5.0.0 |
| ./bwa/bwa-0.7.9a , , | ./bwa/bwa-0.7.9a , mod/version , |
| ./bwa/bwa-0.7.10 , , | ./bwa/bwa-0.7.10 , mod/version , |
| ./bwa/bwa-0.7.17 , https://sourceforge.net/projects/bio-bwa/files/ , 0.7.17 | ./bwa/bwa-0.7.17 , mod/version , 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 | ./bwa-meth/0.2.2 , python bioconda3-el7 bwameth.py , https://github.com/brentp/bwa-meth/releases |
| ./canu/1.3 , , | ./CAFE/4.2.1 , CAFE/4.2.1 , https://github.com/hahnlab/CAFE/releases/tag/v4.2.1 4.2.1 |
| ./canu/1.7 , , | ./canu/1.3 , canu/1.3 , |
| ./canu/2.1 , https://github.com/marbl/canu/releases , 2.1.1 | ./canu/1.7 , canu/1.7 , |
| ./CAP3 , http://seq.cs.iastate.edu/cap3.html , ? | ./canu/2.1 , canu/2.1 , https://github.com/marbl/canu/releases 2.1.1 |
| ./cdhit/v4.6.5 , , | ./CAP3 , mod/version , http://seq.cs.iastate.edu/cap3.html ? |
| ./cdhit/v4.6.8-2017-1208 , https://github.com/weizhongli/cdhit , 4.8.1 | ./cdhit/v4.6.5 , mod/version , |
| ./Celera/(8.1) , https://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/ , 8.3 | ./cdhit/v4.6.8-2017-1208 , mod/version , https://github.com/weizhongli/cdhit 4.8.1 |
| ./clustalw/clustalw-2.1-linux-x86_64-libcppstatic , http://www.clustal.org/download/current/ , 2.1 | ./Celera/(8.1) , mod/version , https://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/ 8.3 |
| ./cnvnator(0.3.3) , , | ./clustalw/clustalw-2.1-linux-x86_64-libcppstatic , mod/version , http://www.clustal.org/download/current/ 2.1 |
| ./CNVnator(0.3.3) , https://github.com/abyzovlab/CNVnator , 0.4.1 | ./cnvnator(0.3.3) , mod/version , |
| ./crb-blast/20151012 , https://github.com/cboursnell/crb-blast , deprecated | ./CNVnator(0.3.3) , mod/version , https://github.com/abyzovlab/CNVnator 0.4.1 |
| ./CroCo/1.1(20180320) , https://github.com/cschmidtlab/croco , 0.7 | ./crb-blast/20151012 , mod/version , https://github.com/cboursnell/crb-blast deprecated |
| ./cufflinks/cufflinks-2.2.1.Linux_x86_64 , , | ./CroCo/1.1(20180320) , croco/1.1 , https://github.com/cschmidtlab/croco 0.7 |
| ./cufflinks/cufflinks-2.2.2 , https://github.com/cole-trapnell-lab/cufflinks/blob/master/README.md , unknown | ./cufflinks/cufflinks-2.2.1.Linux_x86_64 , cufflinks/2.2.1 , |
| ./cutadapt/cutadapt-1.41 , https://cutadapt.readthedocs.io/en/stable/installation.html , 3.2 | ./cufflinks/cufflinks-2.2.2 , mod/version , https://github.com/cole-trapnell-lab/cufflinks/blob/master/README.md unknown |
| ./DataAnalysis/2.8_All , , 2.8 | ./cutadapt/cutadapt-1.41 , cutadapt/1.4.1 , https://cutadapt.readthedocs.io/en/stable/installation.html 3.2 |
| ./datamash/1.0.5 , , | ./DataAnalysis/2.8_All , mod/version , 2.8 |
| ./datamash/1.3 , https://ftp.gnu.org/gnu/datamash/ , 1.7 | ./datamash/1.0.5 , mod/version , |
| ./dDocent , https://www.ddocent.com/downloads/ , 2.7.8 | ./datamash/1.3 , mod/version , https://ftp.gnu.org/gnu/datamash/ 1.7 |
| ./deepTools(2.2.4) , https://github.com/deeptools/deepTools , 3.5.0 | ./dDocent , mod/version , https://www.ddocent.com/downloads/ 2.7.8 |
| ./diamond/0.9.21.122 , , | ./deepTools(2.2.4) , mod/version , https://github.com/deeptools/deepTools 3.5.0 |
| ./diamond/2.0.1 , https://github.com/bbuchfink/diamond , 2.0.6 | ./diamond/0.9.21.122 , diamond/0.9.21.122 , |
| ./dock/dock6 , http://dock.compbio.ucsf.edu/DOCK_6/index.htm , 6.9 | ./diamond/2.0.1 , diamond/2.0.1 , https://github.com/bbuchfink/diamond 2.0.6 |
| ./edirect/8.10 , "https://astrobiomike.github.io/unix/ncbi_eutils , https://www.ncbi.nlm.nih.gov/books/NBK179288/" | ./dock/dock6 , mod/version , http://dock.compbio.ucsf.edu/DOCK_6/index.htm 6.9 |
| ./eigen , use_version_in_share , | ./edirect/8.10 , edirect/8.10 , "https://astrobiomike.github.io/unix/ncbi_eutils https://www.ncbi.nlm.nih.gov/books/NBK179288/" |
| ./emboss/6.6.0 , , | ./eigen , mod/version , use_version_in_share |
| ./emboss/6.6.0-gcc , http://emboss.sourceforge.net/download/#Stable , 6.6.0 | ./emboss/6.6.0 , mod/version , |
| ./EnTAP(20180430) , https://github.com/harta55/EnTAP/ , 0.10.7 | ./emboss/6.6.0-gcc , emboss/6.60 , http://emboss.sourceforge.net/download/#Stable 6.6.0 |
| ./epa-ng/0.3.6 , https://github.com/Pbdas/epa-ng , 0.3.8 | ./EnTAP(20180430) , EnTAP/0.8.1 , https://github.com/harta55/EnTAP/ 0.10.7 |
| ./exonerate/2.2.0 , , | ./epa-ng/0.3.6 , epa-ng/0.3.6 , https://github.com/Pbdas/epa-ng 0.3.8 |
| ./exonerate/2.4.0 , https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate , 2.4.0 | ./exonerate/2.2.0 , mod/version , |
| ./falcon/FALCON-integrate-2016-05 , https://github.com/PacificBiosciences/FALCON , 0.3.0 | ./exonerate/2.4.0 , mod/version , https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate 2.4.0 |
| ./falcon/FALCON-integrate-2018-05 , https://www.pacb.com/support/software-downloads/ , | ./eXpress/1.5.1 , express/1.5.1 , https://pachterlab.github.io/eXpress/overview.html |
| ./FALCON_unzip , , 1.2.0-deprecated | ./falcon/FALCON-integrate-2016-05 , mod/version , https://github.com/PacificBiosciences/FALCON 0.3.0 |
| ./fastqc/FastQC_v0.11.5 , "./bioinformatics/fastqc/FastQC_v0.11.9 , https://www.bioinformatics.babraham.ac.uk/projects/download.html" | ./falcon/FALCON-integrate-2018-05 , mod/version , https://www.pacb.com/support/software-downloads/ |
| ./fastStructure(20170718) , https://rajanil.github.io/fastStructure/ , 1 | ./FALCON_unzip , mod/version , 1.2.0-deprecated |
| ./FastTree/test , , | ./fastANI/1.32 , fastANI/1.32 , https://github.com/ParBLiSS/FastANI 1.32 |
| ./FastTree/2.1.10 , http://www.microbesonline.org/fasttree/#Install , 2.1.11 | ./fastqc/FastQC_v0.11.5 , fastqc/0.11.5 , "./bioinformatics/fastqc/FastQC_v0.11.9 https://www.bioinformatics.babraham.ac.uk/projects/download.html" |
| ./fastx/fastx_toolkit-0.0.1 , https://github.com/agordon/fastx_toolkit , 0.0.14 | ./fastStructure(20170718) , mod/version , https://rajanil.github.io/fastStructure/ 1 |
| ./flash/FLASH-1.2.9 , , | ./FastTree/test , mod/version , |
| ./flash/FLASH-1.2.11 , http://ccb.jhu.edu/software/FLASH/index.shtml , 1.2.11 | ./FastTree/2.1.10 , mod/version , http://www.microbesonline.org/fasttree/#Install 2.1.11 |
| ./Flye/2.6 , https://github.com/fenderglass/Flye , 2.8.2 | ./fastx/fastx_toolkit-0.0.1 , mod/version , https://github.com/agordon/fastx_toolkit 0.0.14 |
| ./gappa/1.3.5 , https://github.com/lczech/gappa , 0.7.0 | ./flash/FLASH-1.2.9 , mod/version , |
| ./GATK/GATK-3.5 , , | ./flash/FLASH-1.2.11 , flash/1.2.11 , http://ccb.jhu.edu/software/FLASH/index.shtml 1.2.11 |
| ./GATK/4.0 , , | ./Flye(2.3.3) , flye/2.3.3 , https://github.com/fenderglass/Flye 2.8.2 |
| ./GATK/gatk-4.0.0.0 , https://github.com/broadinstitute/gatk/releases , 4.1.9.0 | ./Flye/2.6 , flye/2.6 , https://github.com/fenderglass/Flye 2.8.2 |
| ./GCTA/1.91.3beta , https://cnsgenomics.com/software/gcta/#Download , 1.93.2 | ./gappa/1.3.5 , mod/version , https://github.com/lczech/gappa 0.7.0 |
| ./GCTA/build , , | ./GATK/GATK-3.5 , mod/version , |
| ./Gctf/v1.0.6 , https://www2.mrc-lmb.cam.ac.uk/research/locally-developed-software/zhang-software/ , 1.18 | ./GATK/4.0 , gatk/4.0.0 , |
| ./gemma/0.94.1 , , | ./GATK/gatk-4.0.0.0 , mod/version , https://github.com/broadinstitute/gatk/releases 4.1.9.0 |
| ./gemma/0.97 , https://github.com/genetics-statistics/GEMMA , 0.98.4 | ./GCTA/1.91.3beta , mod/version , https://cnsgenomics.com/software/gcta/#Download 1.93.2 |
| ./genometools/1.5.8 , https://github.com/genometools/genometools , unknown | ./GCTA/build , mod/version , |
| ./guppy/2.3.7 , , | ./Gctf/v1.0.6 , mod/version , https://www2.mrc-lmb.cam.ac.uk/research/locally-developed-software/zhang-software/ 1.18 |
| ./guppy/3.2.2-cpu , , | ./gemma/0.94.1 , gemma/0.94.1 , |
| ./guppy/3.2.2-gpu , , | ./gemma/0.97 , gemma/0.97 , https://github.com/genetics-statistics/GEMMA 0.98.4 |
| ./guppy/3.2.4-cpu , , | ./genometools/1.5.8 , genometools/1.5.8 , https://github.com/genometools/genometools unknown |
| ./guppy/3.2.4-gpu , , | ./guppy/2.3.7 , mod/version , |
| ./guppy/4.0.11-gpu(20200708) , login_Oxford_Nanopore , | ./guppy/3.2.2-cpu , mod/version , |
| ./HipSTR/(0.6.1) , https://github.com/tfwillems/HipSTR , 0.7 | ./guppy/3.2.2-gpu , mod/version , |
| ./hisat2/hisat2-2.0.3-beta , , | ./guppy/3.2.4-cpu , mod/version , |
| ./hisat2/hisat2-2.1.0 , , | ./guppy/3.2.4-gpu , mod/version , |
| ./hisat2/hisat2-2.2.1 , http://daehwankimlab.github.io/hisat2/ , 2.2.1/beta-3N | ./guppy/4.0.11-gpu(20200708) , guppy/4.0.11 , login_Oxford_Nanopore |
| ./hmmer/3.1b2 , , | ./guppy/4.4.1-gpu , guppy/4.4.1 , |
| ./hmmer/hmmer-3.1b2 , , | ./guppy/4.4.1-nogpu , guppy/4.4.1 , |
| ./hmmer/hmmer-3.1b2-intel-mvapich , , | ./HipSTR/(0.6.1) , mod/version , https://github.com/tfwillems/HipSTR 0.7 |
| ./hmmer/hmmer-3.1b2-linux-intel-x86_64 , http://hmmer.org/ , 3.2 | ./hisat2/hisat2-2.0.3-beta , hisat2/2.0.3-beta , |
| ./htslib/1.1-pacbio , , | ./hisat2/hisat2-2.1.0 , hisat2/2.1.0 , |
| ./htslib/1.3 , , | ./hisat2/hisat2-2.2.1 , hisat2/2.2.1 , http://daehwankimlab.github.io/hisat2/ 2.2.1/beta-3N |
| ./htslib/1.7 , , | ./hmmer/3.1b2 , mod/version , |
| ./htslib/1.10.2 , http://www.htslib.org/download/ , 1.11 | ./hmmer/hmmer-3.1b2 , mod/version , |
| ./idba/1.1.3 , https://github.com/loneknightpy/idba , 1.1.3 | ./hmmer/hmmer-3.1b2-intel-mvapich , mod/version , |
| ./IGV/IGV_Linux_2.8.0 , https://software.broadinstitute.org/software/igv/download , 2.9.0 | ./hmmer/hmmer-3.1b2-linux-intel-x86_64 , mod/version , http://hmmer.org/ 3.2 |
| ./impute/impute_v2.3.2_x86_64_static , https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#download , 2.3.2 | ./htslib/1.1-pacbio , mod/version , |
| ./infernal/1.1.1-gcc-impi , , | ./htslib/1.3 , mod/version , |
| ./infernal/infernal-1.1.1-linux-intel-gcc , http://eddylab.org/infernal/ , 1.1.4 | ./htslib/1.7 , mod/version , |
| ./iqtree/iqtree-omp-1.5.3-Linux , , | ./htslib/1.10.2 , mod/version , http://www.htslib.org/download/ 1.11 |
| ./iqtree/iqtree-1.6.9-Linux , , | ./idba/1.1.3 , mod/version , https://github.com/loneknightpy/idba 1.1.3 |
| ./iqtree/iqtree-1.6.10-Linux , , | ./igb-5.3.5.4 , mod/version , https://bioviz.org/news.html 9.16 |
| ./iqtree/iqtree-1.6.12-Linux , http://www.iqtree.org/ , 1.6.12 | ./IGV/IGV_Linux_2.8.0 , mod/version , https://software.broadinstitute.org/software/igv/download 2.9.0 |
| ./ISOWN , https://github.com/ikalatskaya/ISOWN , release? | ./impute/impute_v2.3.2_x86_64_static , mod/version , https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#download 2.3.2 |
| ./jellyfish/2.2.6 , , | ./infernal/1.1.1-gcc-impi , infernal/1.1.1 , |
| ./jellyfish/2.3.0 , https://github.com/gmarcais/Jellyfish , 2.3.0 | ./infernal/infernal-1.1.1-linux-intel-gcc , infernal/1.1.1 , http://eddylab.org/infernal/ 1.1.4 |
| ./kallisto/kallisto_linux-v0.43.1 , https://pachterlab.github.io/kallisto/download.html , 0.46.1 | ./iqtree/iqtree-omp-1.5.3-Linux , mod/version , |
| ./khmer/bz2file-0.98-py2.7.egg-info , , | ./iqtree/iqtree-1.6.9-Linux , mod/version , |
| ./khmer/khmer-2.0-py2.7.egg-info , https://github.com/dib-lab/khmer , 2.1.2 | ./iqtree/iqtree-1.6.10-Linux , mod/version , |
| ./khmer/screed-0.9-py2.7.egg-info , , | ./iqtree/iqtree-1.6.12-Linux , mod/version , http://www.iqtree.org/ 1.6.12 |
| ./kmergenie/1.6476 , http://kmergenie.bx.psu.edu/ , 1.7051 | ./ISOWN , isown/1.0 , https://github.com/ikalatskaya/ISOWN release? |
| ./Ktrim/1.1.0 , https://github.com/hellosunking/Ktrim , 1.2.2. | ./jellyfish/2.2.6 , jellyfish/2.2.6 , |
| ./last/last-719 , http://last.cbrc.jp/ , last-1179 | ./jellyfish/2.3.0 , jellyfish/2.3.0 , https://github.com/gmarcais/Jellyfish 2.3.0 |
| ./lordec/lordec-src_0.9 , https://gite.lirmm.fr/lordec/lordec-releases/-/wikis/home , 0.9 | ./kallisto/kallisto_linux-v0.43.1 , mod/version , https://pachterlab.github.io/kallisto/download.html 0.46.1 |
| ./lorma/lorma-src_0.5a , https://gite.lirmm.fr/lorma/lorma-releases/-/wikis/home , 0.5 | ./khmer/bz2file-0.98-py2.7.egg-info , mod/version , |
| ./lsc(1_alpha) , https://web.stanford.edu/group/wonglab/LSC/LSC_download.html , 1.alpha | ./khmer/khmer-2.0-py2.7.egg-info , mod/version , https://github.com/dib-lab/khmer 2.1.2 |
| ./MACSE/v2.03 , https://bioweb.supagro.inra.fr/macse/index.php?menu=releases , 2.0.5 | ./khmer/screed-0.9-py2.7.egg-info , mod/version , |
| ./mafft/7.304 , https://mafft.cbrc.jp/alignment/software/ , 7.475 | ./kmergenie/1.6476 , mod/version , http://kmergenie.bx.psu.edu/ 1.7051 |
| ./maker/2.31.9 , , | ./Ktrim/1.1.0 , mod/version , https://github.com/hellosunking/Ktrim 1.2.2. |
| ./maker/2.31.9b , , | ./last/last-719 , mod/version , http://last.cbrc.jp/ last-1179 |
| ./maker/maker , , | ./lordec/lordec-src_0.9 , mod/version , https://gite.lirmm.fr/lordec/lordec-releases/-/wikis/home 0.9 |
| ./maker/maker-jpummil , http://www.yandell-lab.org/software/maker.html , 3.01.03 | ./lorma/lorma-src_0.5a , mod/version , https://gite.lirmm.fr/lorma/lorma-releases/-/wikis/home 0.5 |
| ./MaSuRCA/3.4.2 , https://github.com/alekseyzimin/masurca , 4.0.1 | ./lsc(1_alpha) , mod/version , https://web.stanford.edu/group/wonglab/LSC/LSC_download.html 1.alpha |
| ./mauve/2015-02-13 , http://darlinglab.org/mauve/user-guide/versions.html , 2.4.0 | ./MACSE/v2.03 , mod/version , https://bioweb.supagro.inra.fr/macse/index.php?menu=releases 2.0.5 |
| ./mcl/12-135 , , | ./mafft/7.304 , mafft/7.304b , https://mafft.cbrc.jp/alignment/software/ 7.475 |
| ./mcl/14-137 , https://micans.org/mcl/src/ , 14-137 | ./maker/maker , maker/2.31.8 , |
| ./megahit/v1.1.3 , https://github.com/voutcn/megahit , 1.2.9 | ./maker/2.31.9b , mod/version , |
| ./meme/meme_4.10.2 , https://meme-suite.org/meme/doc/download.html , 5.3.1 | ./maker/maker-jpummil , mod/version , |
| ./meme/meme-4.10.2 , , | ./maker/2.31.9 , maker/2.31.9 , http://www.yandell-lab.org/software/maker.html 3.01.03 |
| ./MetaGeneMark/MetaGeneMark_linux_64 , , | ./MaSuRCA/3.4.2 , MaSURCA/3.4.2 , https://github.com/alekseyzimin/masurca 4.0.1 |
| ./metaphlan2/2.6.0 , http://huttenhower.sph.harvard.edu/metaphlan , 3 | ./mauve/2015-02-13 , mod/version , http://darlinglab.org/mauve/user-guide/versions.html 2.4.0 |
| ./miniasm , , | ./mcl/12-135 , mod/version , |
| ./minimap2 , , | ./mcl/14-137 , mod/version , https://micans.org/mcl/src/ 14-137 |
| ./minimap2/minimap2-2.10_x64-linux , , | ./megahit/v1.1.3 , megahit/1.1.3 , https://github.com/voutcn/megahit 1.2.9 |
| ./minimap2/2.17 , https://github.com/lh3/minimap2 , 2.1.7 | ./meme/meme_4.10.2 , mod/version , https://meme-suite.org/meme/doc/download.html 5.3.1 |
| ./mira/3.0.5 , https://sourceforge.net/projects/mira-assembler/files/ , 4.0.2 | ./meme/meme-4.10.2 , mod/version , |
| ./miRDeep/mirdeep2_0_0_7 , , | ./MetaGeneMark/MetaGeneMark_linux_64 , mod/version , |
| ./miRDeep/mirdeep2_0_0_8 , https://github.com/rajewsky-lab/mirdeep2 , 0.1.3 | ./methyldactyl/0.5.1 , methyldactyl/0.5.1 , https://github.com/dpryan79/methyldackel |
| ./modeller/9.14 , https://salilab.org/modeller/download_installation.html , 10 | ./migrate-n/migrate-3.6.6 , mod/version , https://peterbeerli.com/migrate-html5/download_version4/ 3.72/4.43 |
| ./mothur/mothur.1.25.0 , , | ./metaphlan2/2.6.0 , mod/version , http://huttenhower.sph.harvard.edu/metaphlan 3 |
| ./mothur/mothur-1.35.1 , , | ./miniasm , miniasm/1.0 , |
| ./mothur/mothur-1.36.1-intel-impi , , | ./minimap2 , mod/version , |
| ./mothur/mothur-1.36.1-serial , , | ./minimap2/minimap2-2.10_x64-linux , minimap2/2.1 , |
| ./mothur/mothur-1.39.1 , , | ./minimap2/2.17 , minimap2/2.17 , https://github.com/lh3/minimap2 2.1.7 |
| ./mothur/mothur-1.39.1-intel-impi , , | ./mira/3.0.5 , mod/version , https://sourceforge.net/projects/mira-assembler/files/ 4.0.2 |
| ./mothur/mothur-1.39.1-serial , , | ./miRDeep/mirdeep2_0_0_7 , miRDeep/2.0.0.7 , |
| ../mothur/mothur-1.39.5-serial , , | ./miRDeep/mirdeep2_0_0_8 , miRDeep/2.0.0.8 , https://github.com/rajewsky-lab/mirdeep2 0.1.3 |
| ../mothur/mothur-1.40.5-serial , , | ./modeller/9.14 , mod/version , https://salilab.org/modeller/download_installation.html 10 |
| ./mothur/1.44.2 , https://github.com/mothur/mothur/releases/tag/v1.44.3 , | ./mothur/mothur.1.25.0 , mod/version , |
| ./mpiblast , , | ./mothur/mothur-1.35.1 , mod/version , |
| ./mrbayes/3.2.6-avx-openmp , , | ./mothur/mothur-1.36.1-intel-impi , mod/version , |
| ./mrbayes/3.2.6-avx-openmp-mpi , , | ./mothur/mothur-1.36.1-serial , mod/version , |
| ./mrbayes/3.2.6-sse-openmp , , | ./mothur/mothur-1.39.1 , mod/version , |
| ./mrbayes/3.2.6-sse-openmp-mpi , http://nbisweden.github.io/MrBayes/download.html , 3.2.7a | ./mothur/mothur-1.39.1-intel-impi , mod/version , |
| ./MultiQC/1.10.dev0 , https://github.com/ewels/MultiQC , 1.9 | ./mothur/mothur-1.39.1-serial , mod/version , |
| ./MUMmer/MUMmer3.23 , https://github.com/mummer4/mummer , 4.0.0 | ./mothur/mothur-1.39.5-serial , mod/version , |
| ./muscle/muscle3.8.31 , http://www.drive5.com/muscle/downloads.htm , 3.8.31 | ./mothur/mothur-1.40.5-serial , mod/version , |
| ./mutect/1.1.7 , https://software.broadinstitute.org/cancer/cga/mutect_download , ?login | ./mothur/1.44.2 , mod/version , https://github.com/mothur/mothur/releases/tag/v1.44.3 |
| ./MutMap/2.1.6 , , | ./mpiblast , mod/version , |
| ./ncbi , , | ./mrbayes/3.2.6-avx-openmp , mrbayes/3.2.6 , |
| ./ncbi/ngs , https://github.com/ncbi/ngs , v? | ./mrbayes/3.2.6-avx-openmp-mpi , mrbayes/3.2.6-mpi , |
| ./ncbi/share , , | ./mrbayes/3.2.6-sse-openmp , mrbayes/3.2.6 , |
| ./ncbi/sra-tools , , | ./mrbayes/3.2.6-sse-openmp-mpi , mrbayes/3.2.6-mpi , http://nbisweden.github.io/MrBayes/download.html 3.2.7a |
| ./ncbi/sra-tools-2.8.1-3 , https://github.com/ncbi/sra-tools/wiki/01.-Downloading-SRA-Toolkit , 2.10.9 | ./MultiQC/1.10.dev0 , mod/version , https://github.com/ewels/MultiQC 1.9 |
| ./newbler(unknown) , , | ./MUMmer/MUMmer3.23 , mod/version , https://github.com/mummer4/mummer 4.0.0 |
| ./newick-utils/1.6 , , | ./muscle/muscle3.8.31 , muscle/3.8.31 , http://www.drive5.com/muscle/downloads.htm 3.8.31 |
| ./nextflow/20.10.0 , , | ./mutect/1.1.7 , mod/version , https://software.broadinstitute.org/cancer/cga/mutect_download ?login |
| ./nim/0.18.0 , https://nim-lang.org/install_unix.html , 1.4.2 | ./MutMap/2.1.6 , mod/version , |
| ./ntedit , , | ./ncbi , mod/version , |
| ./oases/0.2.08 , https://www.ebi.ac.uk/~zerbino/oases/ , 0.2.08 | ./ncbi/ngs , mod/version , https://github.com/ncbi/ngs v? |
| ./OrthoFinder/0.4.0 , , | ./ncbi/share , mod/version , |
| ./OrthoFinder/2.2.6 , , | ./ncbi/sra-tools(2.7.0) , sra-tools/2.7.0 , |
| ./OrthoFinder/2.4.0 , , | ./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 |
| ./OrthoFinder/2.4.0-tmpe , https://github.com/davidemms/OrthoFinder , 2.5.2 | ./ncbi/sra-toolkit.2.9.0 , sra-tools/2.9.0 , |
| ./orthomclSoftware/v2.0.9 , , | ./newbler(unknown) , mod/version , |
| ./PAML/paml4.6 , , | ./newick-utils/1.6 , newick-utils/1.61 , |
| ./PAML/paml4.8 , , | ./nextflow/20.10.0 , nextflow/20.10.0 , |
| ./PAML/paml4.9e , http://abacus.gene.ucl.ac.uk/software/paml.html#download , 4.9 | ./nim/0.18.0 , nim/0.18.0 , https://nim-lang.org/install_unix.html 1.4.2 |
| ./pandaseq , https://github.com/neufeld/pandaseq , 2.11(2017) | ./ntedit , mod/version , |
| ./Panseq , https://github.com/chadlaing/Panseq , 2017 | ./oases/0.2.08 , mod/version , https://www.ebi.ac.uk/~zerbino/oases/ 0.2.08 |
| ./ParGenes , https://github.com/BenoitMorel/ParGenes , 1.2.0 | ./OrthoFinder/0.4.0 , mod/version , |
| ./PASTA/1.8.2 , , | ./OrthoFinder/2.2.6 , orthofinder/2.2.6 , |
| ./PASTA/1.8.3 , https://github.com/smirarab/pasta , python | ./OrthoFinder/2.4.0 , mod/version , |
| ./pbcopper(2016) , https://github.com/PacificBiosciences/pbcopper , 1.9.0(2020) | ./OrthoFinder/2.4.0-tmpe , mod/version , https://github.com/davidemms/OrthoFinder 2.5.2 |
| ./PBSuite/15.8.24 , https://sourceforge.net/projects/pb-jelly/ , 15.8.24 | ./orthomclSoftware/v2.0.9 , mod/version , |
| ./pcit , , | ./PAML/paml4.6 , PAML/4.6 , |
| ./pear/0.9.11 , https://github.com/tseemann/PEAR , 0.9.11 | ./PAML/paml4.8 , PAML/4.8 , |
| ./phylophlan , , | ./PAML/paml4.9e , PAML/4.9e , http://abacus.gene.ucl.ac.uk/software/paml.html#download 4.9 |
| ./phyx-incomplete , https://github.com/FePhyFoFum/phyx , 1.1(2020) | ./pandaseq , mod/version , https://github.com/neufeld/pandaseq 2.11(2017) |
| ./picard/picard-tools-2.1.1 , , | ./Panseq , mod/version , https://github.com/chadlaing/Panseq 2017 |
| ./picard/picard-tools-2.17.10 , https://github.com/broadinstitute/picard/releases/tag/2.24.2 , | ./ParGenes , mod/version , https://github.com/BenoitMorel/ParGenes 1.2.0 |
| ./pilon/1.22 , , | ./PASTA/1.8.2 , mod/version , |
| ./pindel , https://github.com/genome/pindel , 0.2.5b8(2015) | ./PASTA/1.8.3 , mod/version , https://github.com/smirarab/pasta python |
| ./pitchfork , https://github.com/PacificBiosciences/pitchfork , 2017 | ./pbcopper(2016) , mod/version , https://github.com/PacificBiosciences/pbcopper 1.9.0(2020) |
| ./plink/1.90b6.6 , , | ./PBSuite/15.8.24 , PBSuite/15.8.24 , https://sourceforge.net/projects/pb-jelly/ 15.8.24 |
| ./plink/1.90b6.10 , https://www.cog-genomics.org/plink2 , 1.90beta(20201019) | ./pcit , pcit/1.0 , |
| ./plink/3.46 , , | ./pear/0.9.11 , pear/0.9.11 , https://github.com/tseemann/PEAR 0.9.11 |
| ./plink/5.2 , https://www.cog-genomics.org/plink/ , 6.2.1 | ./phylophlan , mod/version , |
| ./pysam/0.9.0 , https://pypi.org/project/pysam/ , | ./phyx-incomplete , mod/version , https://github.com/FePhyFoFum/phyx 1.1(2020) |
| ./quast/quast-5.0.0 , http://quast.sourceforge.net/install.html , 5.0.2 | ./picard/picard-tools-2.1.1 , mod/version , |
| ./randfold/2.0.1 , , | ./picard/picard-tools-2.17.10 , mod/version , https://github.com/broadinstitute/picard/releases/tag/2.24.2 |
| ./raven/1.1.0 , https://github.com/SysBioChalmers/RAVEN , 2.4.2 | ./pilon/1.22 , mod/version , |
| ./RAxML/stamatak-standard-RAxML-5_7_2012 , , | ./pindel , mod/version , https://github.com/genome/pindel 0.2.5b8(2015) |
| ./RAxML/RAXML-8.0.20 , , | ./pitchfork , mod/version , https://github.com/PacificBiosciences/pitchfork 2017 |
| ./RAxML/RAxML-8.2.9 , https://github.com/stamatak/standard-RAxML , 8.2.12 | ./plink/1.90b6.6 , plink/1.90b6.6 , |
| ./RAxML/RAxML-8.2.11 , https://github.com/amkozlov/raxml-ng/releases , 1.0.1 | ./plink/1.90b6.10 , plink/1.90b6.10 , https://www.cog-genomics.org/plink2 1.90beta(20201019) |
| ./Rcorrector(20160212) , https://github.com/mourisl/Rcorrector , 1.0.4(2019) | ./plink/3.46 , plink/3.46 , |
| ./rDock/2013.1 , https://sourceforge.net/projects/rdock/files/?source=navbar , 2013.1 | ./plink/5.2 , plink/5.2 , https://www.cog-genomics.org/plink/ 6.2.1 |
| ./rdp_classifier/2.2 , https://sourceforge.net/projects/rdp-classifier/ , 2.13 | ./pplacer/1.1-alpha19 , , pplacer/1.1-alpha19 https://github.com/matsen/pplacer |
| ./rdp_classifier/2.12 , https://github.com/rdpstaff/classifier , 2.10.2 | ./prodigal/2.6.3 , prodigal/2.6.3 , https://github.com/hyattpd/Prodigal 2.6.3 |
| ./reapr/1.0.17 , https://www.sanger.ac.uk/tool/reapr// , 1.0.18 | ./pysam/0.9.0 , mod/version , https://pypi.org/project/pysam/ |
| ./RepeatMasker/4.0.7 , http://www.repeatmasker.org/ , 4.1.1 | ./quast/quast-5.0.0 , mod/version , http://quast.sourceforge.net/install.html 5.0.2 |
| ./root_digger/1.1.4 , https://github.com/computations/root_digger , 1.7.0 | ./randfold/2.0.1 , mod/version , |
| ./rsem/1.2.27 , , | ./raven/1.1.0 , mod/version , https://github.com/SysBioChalmers/RAVEN 2.4.2 |
| ./rsem/1.3.0 , , | ./RAxML/stamatak-standard-RAxML-5_7_2012 , mod/version , |
| ./rsem/1.3.3 , http://deweylab.github.io/RSEM/ , 1.3.3 | ./RAxML/RAXML-8.0.20 , mod/version , |
| ./rsem/RSEM-1.3.3-install , , | ./RAxML/RAxML-8.2.9 , raxml/8.2.9 , https://github.com/stamatak/standard-RAxML 8.2.12 |
| ./salmon/Salmon-0.8.2_linux_x86_64 , , | ./RAxML/RAxML-8.2.11 , raxml/8.2.11 , https://github.com/amkozlov/raxml-ng/releases 1.0.1 |
| ./salmon/Salmon-0.14.1_linux_x86_64 , , | ./Rcorrector(20160212) , mod/version , https://github.com/mourisl/Rcorrector 1.0.4(2019) |
| ./salmon/1.2.1 , , | ./rDock/2013.1 , mod/version , https://sourceforge.net/projects/rdock/files/?source=navbar 2013.1 |
| ./salmon/1.2.1-install , https://github.com/COMBINE-lab/salmon , 1.4.0 | ./rdp_classifier/2.2 , mod/version , https://sourceforge.net/projects/rdp-classifier/ 2.13 |
| ./sambamba/0.7.1 , https://github.com/biod/sambamba , 0.8.0 | ./rdp_classifier/2.12 , mod/version , https://github.com/rdpstaff/classifier 2.10.2 |
| ./samsa2 , https://github.com/transcript/samsa2 , 2.2.0.1 | ./reapr/1.0.17 , reapr/1.0.17 , https://www.sanger.ac.uk/tool/reapr// 1.0.18 |
| ./samstat/1.5.1 , http://samstat.sourceforge.net/ , 1.5.1 | ./RepeatMasker/4.0.7 , RepeatMasker/4.0.7 , http://www.repeatmasker.org/ 4.1.1 |
| ./samtools/1.3 , , | ./root_digger/1.1.4 , mod/version , https://github.com/computations/root_digger 1.7.0 |
| ./samtools/1.4 , , | ./rsem/1.2.27 , mod/version , |
| ./samtools/1.7 , , | ./rsem/1.3.0 , mod/version , |
| ./samtools/1.9 , , | ./rsem/1.3.3 , mod/version , http://deweylab.github.io/RSEM/ 1.3.3 |
| ./samtools/1.10 , , | ./rsem/RSEM-1.3.3-install , mod/version , |
| ./samtools/bcftools-1.10.2 , , | ./salmon/Salmon-0.8.2_linux_x86_64 , salmon/0.8.2 , |
| ./samtools/htslib-1.10.2 , , | ./salmon/Salmon-0.14.1_linux_x86_64 , salmon/0.14.1 , |
| ./samtools/samtools-0.1.19 , , | ./salmon/1.2.1 , salmon/1.2.1 , |
| ./samtools/samtools-1.9 , , | ./salmon/1.4.0 , salmon/1.4.0 , https://github.com/COMBINE-lab/salmon 1.4.0 |
| ./samtools/samtools-1.10 , http://www.htslib.org/download/ , 1.11 | ./sambamba/0.7.1 , mod/version , https://github.com/biod/sambamba 0.8.0 |
| ./sate-tools-linux/2018-04 , https://github.com/sate-dev/sate-tools-linux , 2013 | ./samsa2 , samsa/2.0 , https://github.com/transcript/samsa2 2.2.0.1 |
| ./sepp/sepp-4.3.5 , , | ./samstat/1.5.1 , mod/version , http://samstat.sourceforge.net/ 1.5.1 |
| ./sepp/sepp-4.3.7 , https://github.com/smirarab/sepp , ? | ./samtools/1.3 , mod/version , |
| ./sepp-tools , , | ./samtools/1.4 , mod/version , |
| ./seqtk , https://github.com/lh3/seqtk , 1.3(2018) | ./samtools/1.7 , mod/version , |
| ./shapeit/extractPIRs , , | ./samtools/1.9 , mod/version , |
| ./shapeit/extractPIRs.v1.r68.x86_64 , , | ./samtools/1.10 , mod/version , |
| ./shapeit/shapeit.v2.904.2.6.32-696.18.7.el6.x86_64 , , | ./samtools/bcftools-1.10.2 , mod/version , |
| ./shapeit/shapeit.v2.904.3.10.0-693.11.6.el7.x86_64 , , | ./samtools/htslib-1.10.2 , mod/version , |
| ./shapeit/r904 , https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#download , r904 | ./samtools/samtools-0.1.19 , mod/version , |
| ./sickle/1.33 , https://github.com/najoshi/sickle , 1.33 | ./samtools/samtools-1.9 , mod/version , |
| ./simple/1.8.1 , https://github.com/wacguy/Simple-1.8.1 , ? | ./samtools/samtools-1.10 , mod/version , http://www.htslib.org/download/ 1.11 |
| ./smrtlink , https://www.pacb.com/support/software-downloads/ , 9 | ./sate-tools-linux/2018-04 , mod/version , https://github.com/sate-dev/sate-tools-linux 2013 |
| ./snap/2013-11-29 , http://korflab.ucdavis.edu/software.html , 2013-11-29 | ./sepp/sepp-4.3.5 , mod/version , |
| ./snpEff , https://pcingola.github.io/SnpEff/ , 4.3T | ./sepp/sepp-4.3.7 , mod/version , https://github.com/smirarab/sepp ? |
| ./SOAPdenovo2/SOAPdenovo2-src-r240-gnu , , | ./sepp-tools , mod/version , |
| ./SOAPdenovo2/SOAPdenovo2-src-r240-intel , https://github.com/aquaskyline/SOAPdenovo2 , 242 | ./seqtk , mod/version , https://github.com/lh3/seqtk 1.3(2018) |
| ./SOAPdenovo-Trans(2011) , https://sourceforge.net/projects/soapdenovotrans/files/SOAPdenovo-Trans/ , 1.0.3(2014) | ./shapeit/extractPIRs , mod/version , |
| ./SomaticSniper , http://gmt.genome.wustl.edu/packages/somatic-sniper/ , 1.0.5.0 | ./shapeit/extractPIRs.v1.r68.x86_64 , mod/version , |
| ./sortmerna/2.1b , https://bioinfo.lifl.fr/RNA/sortmerna/ , 2.1 | ./shapeit/shapeit.v2.904.2.6.32-696.18.7.el6.x86_64 , mod/version , |
| ./spades/SPAdes-3.1.0 , , | ./shapeit/shapeit.v2.904.3.10.0-693.11.6.el7.x86_64 , mod/version , |
| ./spades/SPAdes-3.5.0 , , | ./shapeit/r904 , mod/version , https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#download r904 |
| ./spades/SPAdes-3.6.0 , , | ./sickle/1.33 , mod/version , https://github.com/najoshi/sickle 1.33 |
| ./spades/SPAdes-3.8.1 , , | ./simple/1.8.1 , mod/version , https://github.com/wacguy/Simple-1.8.1 ? |
| ./spades/SPAdes-3.11.1 , , | ./smrt/current , smrt/6.0 , https://www.pacb.com/support/software-downloads/ 9.0 |
| ./spades/SPAdes-3.12.0 , , | ./snap/2013-11-29 , snap/2013-11-29 , http://korflab.ucdavis.edu/software.html 2013-11-29 |
| ./spades/SPAdes-3.14.1 , https://cab.spbu.ru/software/spades/ , 3.15.0 | ./snpEff , mod/version , https://pcingola.github.io/SnpEff/ 4.3T |
| ./sra-tools/2.8.1-3 , , | ./SOAPdenovo2/SOAPdenovo2-src-r240-gnu , soapdenovo2/r240 , |
| ./sratoolkit/2.6.2 , , | ./SOAPdenovo2/SOAPdenovo2-src-r240-intel , soapdenovo2/r240 , https://github.com/aquaskyline/SOAPdenovo2 242 |
| ./sratoolkit/2.9.0 , https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software , 2.10.9 | ./SOAPdenovo-Trans(2011) , mod/version , https://sourceforge.net/projects/soapdenovotrans/files/SOAPdenovo-Trans/ 1.0.3(2014) |
| ./sspace/3.0 , https://github.com/nsoranzo/sspace_basic , | ./SomaticSniper , mod/version , http://gmt.genome.wustl.edu/packages/somatic-sniper/ 1.0.5.0 |
| ./ssu-align/0.1.1 , http://eddylab.org/software/ssu-align/ , 0.1.1 | ./sortmerna/2.1b , mod/version , https://bioinfo.lifl.fr/RNA/sortmerna/ 2.1 |
| ./stacks/1.48 , , | ./spades/SPAdes-3.1.0 , mod/version , |
| ./stacks/2.0B8C , , | ./spades/SPAdes-3.5.0 , mod/version , |
| ./stacks/2.0B9 , , | ./spades/SPAdes-3.6.0 , spades/3.12.0 , |
| ./stacks/2.41 , , | ./spades/SPAdes-3.8.1 , mod/version , |
| ./stacks/2.53 , https://catchenlab.life.illinois.edu/stacks/ , 2.55 | ./spades/SPAdes-3.11.1 , spades/3.12.0 , |
| ./stampy/1.0.23 , https://www.well.ox.ac.uk/research/scientific-cores/bioinformatics-statistical-genetics/software , | ./spades/SPAdes-3.12.0 , spades/3.12.0 , |
| ./STAR/2.5 , , | ./spades/SPAdes-3.14.1 , mod/version , https://cab.spbu.ru/software/spades/ 3.15.0 |
| ./STAR/2.7.3a , https://github.com/alexdobin/STAR , 2.7.7a | ./sra-tools/2.8.1-3 , mod/version , |
| ./strelka/2 , https://github.com/Illumina/strelka , 2.9.10 | ./sratoolkit/2.6.2 , mod/version , |
| ./stringtie/stringtie-2.1.4.Linux_x86_64 , http://www.ccb.jhu.edu/software/stringtie/ , 2.1.4 | ./sratoolkit/2.9.0 , mod/version , https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software 2.10.9 |
| ./structure/2.3.4 , https://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v2.3.4/html/structure.html , 2.3.4 | ./sspace/3.0 , mod/version , https://github.com/nsoranzo/sspace_basic |
| ./subread/subread-2.0.1-Linux-x86_64 , http://subread.sourceforge.net/ , 2.0.1 | ./ssu-align/0.1.1 , mod/version , http://eddylab.org/software/ssu-align/ 0.1.1 |
| ./swig/3.0.10 , http://www.swig.org/ , 4.0.2 | ./stacks/1.48 , mod/version , |
| ./tabix/0.2.5a , , | ./stacks/2.0B8C , mod/version , |
| ./tabix/0.2.5b , Deprecated-see-samtools , | ./stacks/2.0B9 , mod/version , |
| ./tassel/5-standalone , https://bitbucket.org/tasseladmin/tassel-5-standalone/downloads/?tab=tags , 5.2.69 | ./stacks/2.41 , mod/version , |
| ./TopHat/2.1.1a , , | ./stacks/2.53 , mod/version , https://catchenlab.life.illinois.edu/stacks/ 2.55 |
| ./TopHat/2.1.1b , http://ccb.jhu.edu/software/tophat/index.shtml , 2.11 | ./stampy/1.0.23 , mod/version , https://www.well.ox.ac.uk/research/scientific-cores/bioinformatics-statistical-genetics/software |
| ./Tracer/v1.7.1 , https://github.com/beast-dev/tracer/ , 1.7.iii1 | ./STAR/2.5 , mod/version , |
| ./transdecoder/5.5.0 , https://github.com/TransDecoder/TransDecoder/releases , 5.5.0 | ./STAR/2.7.3a , mod/version , https://github.com/alexdobin/STAR 2.7.7a |
| ./trimal/1.4rev22 , https://vicfero.github.io/trimal/index.html , 2.0rev0 | ./strelka/2 , mod/version , https://github.com/Illumina/strelka 2.9.10 |
| ./trimmomatic/Trimmomatic-0.36 , http://www.usadellab.org/cms/index.php?page=trimmomatic , 0.39 | ./stringtie/stringtie-2.1.4.Linux_x86_64 , mod/version , http://www.ccb.jhu.edu/software/stringtie/ 2.1.4 |
| ./trinity/2.10.0 , , | ./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 |
| ./trinity/trinityrnaseq-Trinity-v2.4.0 , , | ./subread/subread-2.0.1-Linux-x86_64 , subread/2.0.1 , http://subread.sourceforge.net/ 2.0.1 |
| ./trinity/trinityrnaseq-v2.10.0 , , | ./swig/3.0.10 , swig/3.0.10 , http://www.swig.org/ 4.0.2 |
| ./trinity/trinityrnaseq-v2.11.0 , https://github.com/trinityrnaseq/trinityrnaseq/releases , 2.11.0 | ./tabix/0.2.5a , mod/version , |
| ./usearch/5.2.236 , , | ./tabix/0.2.5b , mod/version , Deprecated-see-samtools |
| ./usearch/6.1.544 , , | ./tassel/5-standalone , tassel/5.0 , https://bitbucket.org/tasseladmin/tassel-5-standalone/downloads/?tab=tags 5.2.69 |
| ./usearch/8.0.1403 , , | ./TopHat/2.1.1a , mod/version , |
| ./usearch/8.1.1861 , , | ./TopHat/2.1.1b , mod/version , http://ccb.jhu.edu/software/tophat/index.shtml 2.11 |
| ./usearch/10.0.240 , https://www.drive5.com/usearch/download.html , 11.0.667 | ./Tracer/v1.7.1 , mod/version , https://github.com/beast-dev/tracer/ 1.7.iii1 |
| ./VarScan/2.3.9 , https://github.com/dkoboldt/varscan , 2.4.2 | ./transdecoder/5.5.0 , transdecoder/5.5.0 , https://github.com/TransDecoder/TransDecoder/releases 5.5.0 |
| ./vcftools/0.1.15 , https://github.com/vcftools/vcftools , 0.1.16 | ./trimal/1.4rev22 , mod/version , https://vicfero.github.io/trimal/index.html 2.0rev0 |
| ./velvet/velvet_1.2.10 , https://www.ebi.ac.uk/~zerbino/velvet/ , 1.2.10 | ./trimmomatic/Trimmomatic-0.36 , mod/version , http://www.usadellab.org/cms/index.php?page=trimmomatic 0.39 |
| ./ViennaRNA , https://www.tbi.univie.ac.at/RNA/#download , 2.4.17 | ./trinity/2.10.0 , mod/version , trinity/2.10.0 |
| ./vsearch/2.4.0 , https://github.com/torognes/vsearch , 2.15.2 | ./trinity/trinityrnaseq-Trinity-v2.4.0 , mod/version , |
| ./weka/3.8.2 , https://sourceforge.net/projects/weka/files/ , 3.8.5 | ./trinity/trinityrnaseq-v2.10.0 , , |
| ./wgs/wgs-6.1 , deprecated_see_Celera , | ./trinity/trinityrnaseq-v2.11.0 , trinity/group-2.11.0 , |
| ./wombat/180404 , http://didgeridoo.une.edu.au/km/wmbdownload1.php , 25/02/20 | ./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 |
| </csv> | </csv> |
| | |
