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bioinformatics_catalog [2021/02/19 17:37] (current)
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 +===== Bioinformatics Software Catalog =====
 +Not including OpenHPC and other RPM software in /opt and R/python/perl modules
 +<csv>
 +/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
 +</csv>
  
bioinformatics_catalog.txt ยท Last modified: 2021/02/19 17:37 (external edit)