list-of-software
Differences
This shows you the differences between two versions of the page.
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list-of-software [2018/10/21 13:44] – aorth | list-of-software [2023/02/23 12:11] – aorth | ||
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In general you can use the command '' | In general you can use the command '' | ||
- | Otherwise, here is a feeble attempt to list the software we have installed at ILRI, their versions, and (possibly) anyone who has experience running it. We will attempt | + | Otherwise, here is a feeble attempt to list the software we have installed at ILRI, their versions, and (possibly) anyone who has experience running it. We endeavor |
^Name | ^Name | ||
- | |[[abyss-software|abyss]]|2.0.2|'' | ||
|abacas|1.3.1|'' | |abacas|1.3.1|'' | ||
+ | |[[abricate-software|abricate]]|1.0.1|'' | ||
+ | |[[abyss-software|abyss]]|2.1.4|'' | ||
+ | |[[ace-software|ace]]|1.01|'' | ||
|[[ACT-software|ACT]]|13.0.0|'' | |[[ACT-software|ACT]]|13.0.0|'' | ||
|[[admixture-software|admixture]]|1.3.0|'' | |[[admixture-software|admixture]]|1.3.0|'' | ||
Line 17: | Line 19: | ||
|[[angsd-software|angsd]]|0.910|'' | |[[angsd-software|angsd]]|0.910|'' | ||
|[[annovar-software|annovar]]|2016-02-01|'' | |[[annovar-software|annovar]]|2016-02-01|'' | ||
+ | |[[any2fasta-software|any2fasta]]|0.4.2|'' | ||
|apt|1.14.3|'' | |apt|1.14.3|'' | ||
|[[arb-software|arb]]|6.0.3|'' | |[[arb-software|arb]]|6.0.3|'' | ||
|[[artemis-software|artemis]]|16.0.0|'' | |[[artemis-software|artemis]]|16.0.0|'' | ||
+ | |[[artic-tools-software|artic-tools]]|0.3.1|'' | ||
|[[augustus-software|augustus]]|3.3|'' | |[[augustus-software|augustus]]|3.3|'' | ||
+ | |[[awscli-software|awscli]]|2.4.0|'' | ||
|[[bam-readcount-software|bam-readcount]]|0.8.0|'' | |[[bam-readcount-software|bam-readcount]]|0.8.0|'' | ||
|[[bamtools-software|bamtools]]|2.5.1|'' | |[[bamtools-software|bamtools]]|2.5.1|'' | ||
+ | |[[barrnap-software|barrnap]]|0.9|'' | ||
|bayescan|2.1|'' | |bayescan|2.1|'' | ||
- | |[[bcftools-software|bcftools]]|1.8|'' | + | |[[bbmap-software|bbmap]]|38.95|'' |
- | |[[beagle-software|beagle]]|3.0.2|'' | + | |[[bcftools-software|bcftools]]|1.15.1|'' |
- | |[[beast-software|beast]]|1.8.3|'' | + | |bcl2fastq|2.20.0.422|'' |
+ | |[[beagle-software|beagle]]|3.1.2|'' | ||
+ | |[[beast-software|beast]]|1.10.4|'' | ||
+ | |[[beast2-software|beast2]]|2.6.4|'' | ||
|[[bedops-software|bedops]]|2.4.29|'' | |[[bedops-software|bedops]]|2.4.29|'' | ||
- | |[[bedtools-software|bedtools]]|2.25.0|'' | + | |[[bedtools-software|bedtools]]|2.29.0|'' |
|[[binpacker-software|binpacker]]|1.0|'' | |[[binpacker-software|binpacker]]|1.0|'' | ||
|[[bioperl-software|bioperl]]|1.7.2|'' | |[[bioperl-software|bioperl]]|1.7.2|'' | ||
|[[bitseq-software|bitseq]]|0.7.5|'' | |[[bitseq-software|bitseq]]|0.7.5|'' | ||
|[[blasr-software|blasr]]|smrtanalysis-4.0.0|'' | |[[blasr-software|blasr]]|smrtanalysis-4.0.0|'' | ||
- | |[[blast-software|blast]]|2.6.0+|'' | + | |[[blast-software|blast]]|2.12.0+|'' |
|[[blobtools-software|blobtools]]|0.9.19.3|'' | |[[blobtools-software|blobtools]]|0.9.19.3|'' | ||
- | |blat|06-Aug-2013|'' | + | |[[blat-software|blat]]|37x1|'' |
- | |[[bowtie-software|bowtie1 ]]|1.1.1|'' | + | |[[bmtagger-software|bmtagger]]|0.3.102.4|'' |
- | |[[bowtie2-software|bowtie2 ]]|2.3.4.1|'' | + | |[[bowtie-software|bowtie1]]|1.2.3|'' |
+ | |[[bowtie2-software|bowtie2]]|2.5.0|'' | ||
|[[brig-software|brig]]|0.95|'' | |[[brig-software|brig]]|0.95|'' | ||
- | |[[busco-software|BUSCO ]]|3.0.2|'' | + | |[[busco-software|BUSCO ]]|5.2.2|'' |
- | |[[bwa-software|bwa]]|0.7.15|'' | + | |[[bwa-software|bwa]]|0.7.17|'' |
|[[cafe-software|cafe]]|4.1|'' | |[[cafe-software|cafe]]|4.1|'' | ||
|cangs|1.1|'' | |cangs|1.1|'' | ||
- | |[[canu-software|canu]]|1.6|'' | + | |[[canu-software|canu]]|1.8|'' |
|cap3|latest|'' | |cap3|latest|'' | ||
- | |[[cd-hit-software|cd-hit]]|4.6.6|'' | + | |[[ccmetagen-software|ccmetagen]]|1.4.0|'' |
+ | |[[cd-hit-software|cd-hit]]|4.8.1|'' | ||
|[[cegma-software|cegma]]|v2.5|'' | |[[cegma-software|cegma]]|v2.5|'' | ||
|celera-wgs|6.1|'' | |celera-wgs|6.1|'' | ||
|censor|4.2.28|'' | |censor|4.2.28|'' | ||
- | |[[changeo-software|changeo]]|0.3.9|'' | + | |[[centrifuge-software|centrifuge]]|1.0.4|'' |
- | |[[circos-software|circos]]|0.67|'' | + | |[[changeo-software|changeo]]|1.2.0|'' |
+ | |[[checkm-software|checkm]]|1.1.2|'' | ||
+ | |[[circos-software|circos]]|0.69-9|'' | ||
|[[clonalframe-software|clonalframe]]|1.2|'' | |[[clonalframe-software|clonalframe]]|1.2|'' | ||
|[[clonalframeml-software|clonalframeml]]|1.0|'' | |[[clonalframeml-software|clonalframeml]]|1.0|'' | ||
Line 57: | Line 70: | ||
|[[cnvnator-software|CNVnator]]|0.3.3|'' | |[[cnvnator-software|CNVnator]]|0.3.3|'' | ||
|consed|20.0|'' | |consed|20.0|'' | ||
+ | |[[cooler-software|cooler]]|0.8.10|'' | ||
|[[coperead-software|COPEread]]|1.1.2|'' | |[[coperead-software|COPEread]]|1.1.2|'' | ||
|[[corset-software|corset]]|1.06|'' | |[[corset-software|corset]]|1.06|'' | ||
|cufflinks|2.2.1|'' | |cufflinks|2.2.1|'' | ||
- | |[[cutadapt-software|cutadapt]]|v1.8.1|'' | + | |[[cutadapt-software|cutadapt]]|3.5|'' |
+ | |[[czid-cli-software|czid-cli]]|3.0.2|'' | ||
+ | |[[dextractor-software|dextractor]]|git-a7f50c52|'' | ||
|dendroscope|2.7.4|'' | |dendroscope|2.7.4|'' | ||
- | |[[diamond-software|diamond]]|0.9.9|'' | + | |[[diamond-software|diamond]]|2.0.14|'' |
- | |[[ea-utils-software|ea-utils]]|1.1.2|'' | + | |[[drep-software|drep]]|2.5.4|'' |
+ | |[[ea-utils-software|ea-utils]]|1.04.807|'' | ||
+ | |[[eagle-software|eagle]]|2.4.1|'' | ||
|[[edirect-software|edirect]]| 7.80 | '' | |[[edirect-software|edirect]]| 7.80 | '' | ||
+ | |[[eggnog-mapper-software|eggnog-mapper]]| 2.1.9 | '' | ||
|eigenstrat|3.0|'' | |eigenstrat|3.0|'' | ||
+ | |[[emblmygff3-software|emblmygff3]]|2.1|'' | ||
|[[emboss-software|emboss]]|6.6.0|'' | |[[emboss-software|emboss]]|6.6.0|'' | ||
|[[easer-software|easer]]|1.7.0|'' | |[[easer-software|easer]]|1.7.0|'' | ||
Line 71: | Line 91: | ||
|[[exabayes-software|exabayes]]|1.4.1|'' | |[[exabayes-software|exabayes]]|1.4.1|'' | ||
|[[express-software|express]]|1.5.1|'' | |[[express-software|express]]|1.5.1|'' | ||
+ | |[[falco-software|falco]]|0.3.0|'' | ||
+ | |[[falcon-phase-software|falcon-phase]]|git-7c50154e|'' | ||
+ | |[[fastANI-software|fastANI]]|1.3|'' | ||
+ | |[[fastp-software|fastp]]|0.22.0|'' | ||
|[[fastPHASE-software|fastPHASE]]|1.4.8|'' | |[[fastPHASE-software|fastPHASE]]|1.4.8|'' | ||
- | |[[fastqc-software|fastqc]]|0.11.7|'' | + | |[[fastqc-software|fastqc]]|0.11.9|'' |
|[[faststructure-software|fastSTRUCTURE]]|1.0|'' | |[[faststructure-software|fastSTRUCTURE]]|1.0|'' | ||
+ | |[[fasttree-software|fasttree]]|2.1.11|'' | ||
|[[fastx-toolkit-software|fastx_toolkit]]|0.0.13|'' | |[[fastx-toolkit-software|fastx_toolkit]]|0.0.13|'' | ||
|figtree|1.4.0|'' | |figtree|1.4.0|'' | ||
Line 81: | Line 106: | ||
|[[flexbar-software|flexbar]]|2.7.0|'' | |[[flexbar-software|flexbar]]|2.7.0|'' | ||
|[[flux-capacitor-software|flux-capacitor]]|1.6.1|'' | |[[flux-capacitor-software|flux-capacitor]]|1.6.1|'' | ||
+ | |[[flye-software|flye]]|2.9|'' | ||
|frappe|1.1|'' | |frappe|1.1|'' | ||
- | |[[fraggenescan-software|FragGeneScan ]]|1.19|'' | + | |[[fraggenescan-software|FragGeneScan ]]|1.30|'' |
- | |[[freebayes-software|FreeBayes | + | |[[freebayes-software|freebayes]]|1.3.4|'' |
+ | |[[funannotate-software|funannotate]]|1.8.11|See software page| | | ||
|[[gassflow-software|GassFlow ]]|1.0|'' | |[[gassflow-software|GassFlow ]]|1.0|'' | ||
- | |[[gatk-software|GATK ]]|4.0.10.1|'' | + | |[[gatk-software|gatk]]|4.3.0.0|'' |
|[[gapfiller-software|gapfiller]]|1.10|'' | |[[gapfiller-software|gapfiller]]|1.10|'' | ||
|[[geneid-software|geneid]]|1.4.4|'' | |[[geneid-software|geneid]]|1.4.4|'' | ||
+ | |[[genometools-software|genometools]]|1.6.1|'' | ||
+ | |[[genomeworks-software|genomeworks]]|git-baab5668|'' | ||
|[[genscan-software|genscan]]|latest|'' | |[[genscan-software|genscan]]|latest|'' | ||
|[[gffread-software|gffread]]|0.9.6|'' | |[[gffread-software|gffread]]|0.9.6|'' | ||
Line 93: | Line 122: | ||
|glu|1.0b3-prerelease4|'' | |glu|1.0b3-prerelease4|'' | ||
|[[gmap-software|gmap]]|2015-12-31|'' | |[[gmap-software|gmap]]|2015-12-31|'' | ||
+ | |[[graphlan-software|graphlan]]|1.1.3|'' | ||
+ | |[[graphmap-software|graphmap]]|0.5.2|'' | ||
|[[grom-rd-software|grom-rd]]|1.0|'' | |[[grom-rd-software|grom-rd]]|1.0|'' | ||
|[[gromacs-software|gromacs]]|2018.2|'' | |[[gromacs-software|gromacs]]|2018.2|'' | ||
|[[groovy-software|groovy]]|2.4.9|'' | |[[groovy-software|groovy]]|2.4.9|'' | ||
|[[gsea-software|GSEA]]|2.2.3|'' | |[[gsea-software|GSEA]]|2.2.3|'' | ||
+ | |[[gtdbtk-software|gtdbtk]]|1.1.1|'' | ||
|[[guidance-software|guidance]]|2.02|'' | |[[guidance-software|guidance]]|2.02|'' | ||
+ | |[[guppy-software|guppy]]|6.2.1|'' | ||
+ | |[[halcyon-software|halcyon]]|0.1.1|'' | ||
|[[hapflk-software|hapflk]]|1.4|'' | |[[hapflk-software|hapflk]]|1.4|'' | ||
|hapmix|2.0|'' | |hapmix|2.0|'' | ||
+ | |[[hawk-software|hawk]]|git-a177811d|'' | ||
+ | |[[hclust2-software|hclust2]]|1.0.0|'' | ||
|[[hdf5-software|hdf5]]|1.8.19|'' | |[[hdf5-software|hdf5]]|1.8.19|'' | ||
- | |[[hmmer-software|hmmer]]|3.1b2|'' | + | |[[hmmer-software|hmmer]]|3.3|'' |
+ | |[[hmmIBD-software|hmmIBD]]|2.0.4|'' | ||
|[[hpg-variant-software|hpg-variant]]|1.0|'' | |[[hpg-variant-software|hpg-variant]]|1.0|'' | ||
+ | |[[hic_qc-software|hic_qc]]|git-1e132fb2|'' | ||
+ | |[[hifiasm-software|hifiasm]]|0.16.1|'' | ||
|[[hisat2-software|hisat2]]|2.1.0|'' | |[[hisat2-software|hisat2]]|2.1.0|'' | ||
- | |[[htseq-software|htseq]]|0.6.1|'' | + | |[[htseq-software|htseq]]|0.9.1|'' |
- | |[[htslib-software|htslib]]|1.8|'' | + | |[[htslib-software|htslib]]|1.15.1|'' |
- | |[[igblast-software|igblast]]|1.6.0|'' | + | |[[hypo-software|hypo]]|1.0.3|'' |
+ | |[[idba-software|idba]]|1.1.2|'' | ||
+ | |[[igblast-software|igblast]]|1.10.0|'' | ||
+ | |[[igdiscover-software|igdiscover]]|0.12.3|'' | ||
|[[igrec-software|igrec]]|3.0.0|'' | |[[igrec-software|igrec]]|3.0.0|'' | ||
+ | |[[igsimulator-software|igsimulator]]|git-c3778b74|'' | ||
+ | |[[iqtree-software|iqtree]]|2.2.0|'' | ||
|[[igv-software|igv]]|2.4.5|'' | |[[igv-software|igv]]|2.4.5|'' | ||
|[[igvtools-software|igvtools]]|2.3.98|'' | |[[igvtools-software|igvtools]]|2.3.98|'' | ||
+ | |[[infernal-software|infernal]]|1.1.2|'' | ||
|[[interproscan-software|interproscan]]|5.13|'' | |[[interproscan-software|interproscan]]|5.13|'' | ||
|i-tasser|latest|'' | |i-tasser|latest|'' | ||
- | |[[java-software|java]]|1.8|'' | + | |[[ivar-software|ivar]]|1.3.1|'' |
- | |[[jellyfish-software|jellyfish]]|2.2.9|'' | + | |[[jellyfish-software|jellyfish]]|2.3.0|'' |
|jMHC|1.5.0929|'' | |jMHC|1.5.0929|'' | ||
- | |julia|v0.1.2|'' | + | |[[juicebox-software|juicebox]]|1.11.08|'' |
- | |[[kaiju-software|kaiju]]|1.4.4|'' | + | |[[juicer-software|juicer]]|1.6|'' |
+ | |[[kaiju-software|kaiju]]|1.8.2|'' | ||
|[[kallisto-software|kallisto]]|0.43.0|'' | |[[kallisto-software|kallisto]]|0.43.0|'' | ||
+ | |[[karect-software|karect]]|1.0|'' | ||
|[[kat-software|kat]]|2.3.4|'' | |[[kat-software|kat]]|2.3.4|'' | ||
+ | |[[kma-software|kma]]|1.4.11|'' | ||
+ | |[[kmc-software|kmc]]|3.1.1|'' | ||
|[[kmergenie-software|kmergenie]]|1.7038|'' | |[[kmergenie-software|kmergenie]]|1.7038|'' | ||
|[[kmer-ssr-software|kmer-ssr]]|git-4043c0e7|'' | |[[kmer-ssr-software|kmer-ssr]]|git-4043c0e7|'' | ||
- | |[[kraken-software|kraken]]|0.10.5|'' | + | |[[kraken-software|kraken]]|2.1.2|'' |
- | |krona|2.4|'' | + | |[[krona-software|krona]]|2.8.1|'' |
|lamp|2.5|'' | |lamp|2.5|'' | ||
|lava|0.1|'' | |lava|0.1|'' | ||
|ldhat|2.1|'' | |ldhat|2.1|'' | ||
|[[libsvm-software|libsvm]]|3.20|'' | |[[libsvm-software|libsvm]]|3.20|'' | ||
+ | |[[lighter-software|lighter]]|1.1.2|'' | ||
+ | |[[longshot-software|longshot]]|0.4.5|'' | ||
+ | |[[lordec-software|lordec]]|0.9|'' | ||
+ | |[[ltr_retriever-software|ltr_retriever]]|2.9.0|'' | ||
|lucy|1.19p|'' | |lucy|1.19p|'' | ||
- | |[[mafft-software|mafft]]|7.313|'' | + | |[[mafft-software|mafft]]|7.475|'' |
+ | |[[maker-software|maker]]|3.01.03|'' | ||
|[[mapsplice-software|mapsplice]]|2.2.0|'' | |[[mapsplice-software|mapsplice]]|2.2.0|'' | ||
- | |[[mash-software|mash]]|2.0|'' | + | |[[marginalign-software|marginalign]]|git-2369dafd|'' |
+ | |[[marginpolish-software|marginpolish]]|1.0.0|'' | ||
+ | |[[mash-software|mash]]|2.2|'' | ||
+ | |[[masurca-software|masurca]]|3.3.1|'' | ||
|mauve|2.3.1|'' | |mauve|2.3.1|'' | ||
- | |[[masurca-software|masurca]]|2.3.2|'' | + | |[[maxbin2-software|maxbin2]]|2.2.7|'' |
|maximus|0.2|'' | |maximus|0.2|'' | ||
|[[mcl-software|mcl]]|14-137|'' | |[[mcl-software|mcl]]|14-137|'' | ||
- | |[[megahit-software|megahit]]|git-02102e1b|'' | + | |[[mcscanx-software|mcscanx]]|git-97e74f40|'' |
+ | |[[mecat-software|MECAT]]|git-d04bfa84|'' | ||
+ | |[[medaka-software|medaka]]|1.4.3|'' | ||
+ | |[[megahit-software|megahit]]|1.2.9|'' | ||
|megan|4.70.4|'' | |megan|4.70.4|'' | ||
+ | |[[megax-software|megax]]|10.0.5|'' | ||
|[[metabat-software|metabat]]|2.12.1|'' | |[[metabat-software|metabat]]|2.12.1|'' | ||
+ | |[[metaeuk-software|metaeuk]]|git-9818d1a5|'' | ||
+ | |[[metaphlan-software|metaphlan]]|3.0.13|'' | ||
|[[metis-software|metis]]|5.1.0|'' | |[[metis-software|metis]]|5.1.0|'' | ||
|[[migec-software|migec]]|1.2.4a|'' | |[[migec-software|migec]]|1.2.4a|'' | ||
|[[migmap-software|migmap]]|1.0.2|'' | |[[migmap-software|migmap]]|1.0.2|'' | ||
+ | |[[miniasm-software|miniasm]]|0.3|'' | ||
+ | |[[minimac3-software|minimac3]]|2.0.1|'' | ||
+ | |[[minimac4-software|minimac4]]|1.0.3|'' | ||
+ | |[[minimap2-software|minimap2]]|2.24|'' | ||
|[[minpath-software|MinPath]]|1.0.2|'' | |[[minpath-software|MinPath]]|1.0.2|'' | ||
- | |[[mira-software# | + | |[[mira-software# |
+ | |[[mirdeep2-software|mirdeep2]]|0.1.3|'' | ||
|[[mitools-software|mitools]]|1.4|'' | |[[mitools-software|mitools]]|1.4|'' | ||
- | |[[mixcr-software|mixcr]]|2.0.1|'' | + | |[[mixcr-software|mixcr]]|3.0.11|'' |
|mkatari-ilri|latest|'' | |mkatari-ilri|latest|'' | ||
|[[modeller-software|modeller]]|9.17|'' | |[[modeller-software|modeller]]|9.17|'' | ||
- | |[[mothur-software|mothur]]|1.39.5|'' | + | |[[mosdepth-software|mosdepth]]|0.2.9|'' |
+ | |[[mothur-software|mothur]]|1.44.1|'' | ||
|[[mothur-krona-software|mothur-krona]]|git-87499a0|'' | |[[mothur-krona-software|mothur-krona]]|git-87499a0|'' | ||
|mpiblast|1.6.0|'' | |mpiblast|1.6.0|'' | ||
|mrbayes|3.2.2|'' | |mrbayes|3.2.2|'' | ||
- | |[[multiqc-software|multiqc]]|1.4|'' | + | |[[multiqc-software|multiqc]]|1.12|'' |
- | |[[muscle-software|muscle]]|3.8.31|'' | + | |[[muscle-software|muscle]]|3.8.1551|'' |
- | |[[mummer-software|MUMmer]]|3.23|'' | + | |[[mummer-software|mummer]]|4.0.0rc1|'' |
+ | |[[nanopolish-software|nanopolish]]|0.14.0|'' | ||
|[[netmhcpan-software|netmhcpan]]|2.8|'' | |[[netmhcpan-software|netmhcpan]]|2.8|'' | ||
+ | |[[nextalign-software|nextalign]]|1.11.0|'' | ||
+ | |[[nextclade-software|nextclade]]|1.11.0|'' | ||
|[[nextclip-software|nextclip]]|1.3.1|'' | |[[nextclip-software|nextclip]]|1.3.1|'' | ||
+ | |[[nextflow-software|nextflow]]|21.10 (21.10.6)|'' | ||
+ | |[[ngs-tools-software|ngs-tools]]|3.0.0|'' | ||
|[[ntcard-software|ntCard]]|1.0.0|'' | |[[ntcard-software|ntCard]]|1.0.0|'' | ||
+ | |[[ngmlr-software|ngmlr]]|0.2.7|'' | ||
|[[ngsqctoolkit-software|ngsqctoolkit]]|2.3.3|'' | |[[ngsqctoolkit-software|ngsqctoolkit]]|2.3.3|'' | ||
+ | |[[nQuire-software|nQuire]]|git-a990a88e|'' | ||
+ | |[[nvtop-software|nvtop]]|2.0.2|'' | ||
|novacraft|3.02.07|'' | |novacraft|3.02.07|'' | ||
|[[oases-software|oases]]|0.2.08|'' | |[[oases-software|oases]]|0.2.08|'' | ||
- | |[[ocaml-software# | + | |[[ocaml-software# |
- | |[[opam-software# | + | |[[oligoarrayaux-software|oligoarrayaux]]|3.8.1|'' |
+ | |[[opam-software# | ||
|orthomcl|2.0.3|'' | |orthomcl|2.0.3|'' | ||
+ | |[[orp-software|Oyster River Protocol]]|2.2.8|'' | ||
|[[pagan-software|pagan]]|0.61|'' | |[[pagan-software|pagan]]|0.61|'' | ||
|[[pairfq-software|pairfq]]|0.14.4|'' | |[[pairfq-software|pairfq]]|0.14.4|'' | ||
Line 168: | Line 247: | ||
|[[pandaseq-software|pandaseq]]|2.8.1|'' | |[[pandaseq-software|pandaseq]]|2.8.1|'' | ||
|[[pasta-software|pasta]]|d939adb2|'' | |[[pasta-software|pasta]]|d939adb2|'' | ||
- | |[[pear-software|pear]]|git-2c309dc|'' | + | |[[pathoscope-software|pathoscope]]|2.0.7|'' |
+ | |[[pear-software|pear]]|0.9.6|'' | ||
+ | |[[pblat-software|pblat]]|2.1|'' | ||
|[[pbsuite-software|pbsuite]]|15.8.24|'' | |[[pbsuite-software|pbsuite]]|15.8.24|'' | ||
- | |[[perl-software|perl]]|5.22.3|'' | + | |[[perl-software|perl]]|5.28.2|'' |
|[[pgdspider-software|PGDSpider]]|2.1.1.0|'' | |[[pgdspider-software|PGDSpider]]|2.1.1.0|'' | ||
|phrap|1.080812|'' | |phrap|1.080812|'' | ||
Line 176: | Line 257: | ||
|[[phylip-software|phylip]]|3.696|'' | |[[phylip-software|phylip]]|3.696|'' | ||
|[[phyml-software|phyml]]|3.3.20180621|'' | |[[phyml-software|phyml]]|3.3.20180621|'' | ||
- | |[[picard-software|picard]]|2.17.0|'' | + | |[[picard-software|picard]]|2.27.5|'' |
|[[picrust-software# | |[[picrust-software# | ||
+ | |[[pilon-software|pilon]]|1.23|'' | ||
+ | |[[plasmidid-software|plasmidid]]|1.6.3|'' | ||
|[[platanus-software|platanus]]|1.2.1|'' | |[[platanus-software|platanus]]|1.2.1|'' | ||
- | |[[plink-software|plink]]|1.9|'' | + | |[[plink-software|plink]]|2.00-alpha|'' |
|[[polyphen-software|polyphen]]|2.2.2|'' | |[[polyphen-software|polyphen]]|2.2.2|'' | ||
+ | |[[poplddecay-software|poplddecay]]|3.41|'' | ||
+ | |[[porechop-software|porechop]]|0.3.2pre|'' | ||
+ | |[[pplacer-software|pplacer]]|1.1.alpha19|'' | ||
|[[prank-software|prank]]|170427|'' | |[[prank-software|prank]]|170427|'' | ||
- | |[[presto-software|presto]]|0.5.3|'' | + | |[[presto-software|presto]]|0.5.13|'' |
+ | |[[primalscheme-software|primalscheme]]|1.3.2|'' | ||
|primer3|2.3.6|'' | |primer3|2.3.6|'' | ||
- | |[[prokka-software|prokka]]|1.11|'' | + | |[[prinseq-software|prinseq]]|0.20.4|'' |
+ | |[[prodigal-software|prodigal]]|2.6.3|'' | ||
+ | |[[prokka-software|prokka]]|1.14.6|'' | ||
|[[provean-software|provean]]|1.1.5|'' | |[[provean-software|provean]]|1.1.5|'' | ||
- | |[[python-software|python]]|3.6.2|'' | + | |[[purge-haplotigs-software|purge_haplotigs]]|1.1.1|'' |
+ | |[[python-software|python]]|3.9.14|'' | ||
|qdd|3_beta|'' | |qdd|3_beta|'' | ||
|[[qiime-software|qiime]]|1.9.1|'' | |[[qiime-software|qiime]]|1.9.1|'' | ||
- | |[[qiime2-software|qiime2]]|2018.6|'' | + | |[[qiime2-software|qiime2]]|2021.8|'' |
- | |[[quast-software|quast]]|4.5|'' | + | |[[quast-software|quast]]|5.0.2|'' |
+ | |[[quickmerge-software|quickmerge]]|0.3|'' | ||
|[[quorum-software|Quorum]]|1.1.1|'' | |[[quorum-software|Quorum]]|1.1.1|'' | ||
- | |[[r-software|R]]|3.5.1|'' | + | |[[r-software|R]]|4.2.0|'' |
- | |[[rmblast-software|rmblast]]|2.2.28|'' | + | |[[racon-software|racon]]|1.3.1|'' |
- | |rstudio|v0.97.551|'' | + | |[[rapsearch-software|rapsearch]]|2.22|'' |
- | |rapsearch|2.10|'' | + | |
|[[ratt-software|RATT]]|r18|'' | |[[ratt-software|RATT]]|r18|'' | ||
|[[raxml-software|RAxML]]|8.2.12|'' | |[[raxml-software|RAxML]]|8.2.12|'' | ||
|[[ray-software|ray]]|2.3.1|'' | |[[ray-software|ray]]|2.3.1|'' | ||
+ | |[[rcorrector-software|rcorrector]]|1.0.5|'' | ||
|[[rdp-classifier-software|RDP Classifier]]|2.11|'' | |[[rdp-classifier-software|RDP Classifier]]|2.11|'' | ||
- | |repeatmasker|4.0.5|'' | + | |[[recon-software|recon]]|1.08|'' |
+ | |[[repeatmasker-software|repeatmasker]]|4.1.2-p1|'' | ||
+ | |[[repeatmodeler-software|repeatmodeler]]|2.0.1|'' | ||
+ | |[[repseqio-software|repseqio]]|1.3.3|'' | ||
+ | |[[rgi-software|rgi]]|6.0.2|'' | ||
+ | |[[rmblast-software|rmblast]]|2.11.0|'' | ||
|[[root-software|root]]|6.08.06|'' | |[[root-software|root]]|6.08.06|'' | ||
|[[rrnaselector-software|rRNASelector]]|1.1|'' | |[[rrnaselector-software|rRNASelector]]|1.1|'' | ||
- | |[[rsem-software|RSEM]]|1.2.21|'' | + | |[[rsem-software|RSEM]]|1.3.1|'' |
|[[rseqc-software|rseqc]]|2.6.4|'' | |[[rseqc-software|rseqc]]|2.6.4|'' | ||
|[[ruby-software|ruby]]|2.2.3|'' | |[[ruby-software|ruby]]|2.2.3|'' | ||
- | |[[samtools-software|samtools]]|1.8|'' | + | |[[samtools-software|samtools]]|1.15.1|'' |
|[[sailfish-software|sailfish]]|0.9.2|'' | |[[sailfish-software|sailfish]]|0.9.2|'' | ||
- | |[[salmon-software|salmon]]|0.9.1|'' | + | |[[salmon-software|salmon]]|1.3.0|'' |
+ | |[[salsa-software|salsa]]|git-974589f3|'' | ||
+ | |[[satsuma2-software|satsuma2]]|git-37c5f386|'' | ||
|[[scipio-software|scipio]]|1.4.1|'' | |[[scipio-software|scipio]]|1.4.1|'' | ||
|[[scythe-software|scythe]]|0.994-beta|'' | |[[scythe-software|scythe]]|0.994-beta|'' | ||
+ | |[[sepp-software|sepp]]|4.5.1|'' | ||
+ | |[[seroba-software|seroba]]|1.0.0|'' | ||
|seq_crumbs|0.1.8|'' | |seq_crumbs|0.1.8|'' | ||
- | |[[seqkit-software|seqkit]]|0.7.2|'' | + | |[[seqkit-software|seqkit]]|0.11.0|'' |
|[[seqqs-software|seqqs]]|git-3d053750|'' | |[[seqqs-software|seqqs]]|git-3d053750|'' | ||
- | |[[seqtk-software|seqtk]]|1.2-r102|'' | + | |[[seqtk-software|seqtk]]|1.3|'' |
+ | |[[seqwish-software|seqwish]]|0.6|'' | ||
|[[shannon-software|shannon]]|0.0.2|'' | |[[shannon-software|shannon]]|0.0.2|'' | ||
+ | |[[shannon_cpp-software|shannon_cpp]]|0.5.0|'' | ||
+ | |[[shasta-software|shasta]]|0.4.0|'' | ||
|[[sickle-software|sickle]]|1.33|'' | |[[sickle-software|sickle]]|1.33|'' | ||
|[[sift-software|sift]]|4.0.3b|'' | |[[sift-software|sift]]|4.0.3b|'' | ||
|[[sistr-software|sistr]]|1.0.2|'' | |[[sistr-software|sistr]]|1.0.2|'' | ||
|[[smalt-software|smalt]]|0.7.6|'' | |[[smalt-software|smalt]]|0.7.6|'' | ||
+ | |[[smartdenovo-software|smartdenovo]]|git-5cc1356b|'' | ||
+ | |[[snakemake-software|snakemake]]|6.15.5|'' | ||
+ | |[[sniffles-software|sniffles]]|1.0.12b|'' | ||
|snowhite|1.1.4|'' | |snowhite|1.1.4|'' | ||
|[[snpeff-software|SnpEff & SnpSift]]|4.1g|'' | |[[snpeff-software|SnpEff & SnpSift]]|4.1g|'' | ||
Line 230: | Line 336: | ||
|[[soapdenovo-trans-software|SOAPdenovo-Trans]]|1.03|'' | |[[soapdenovo-trans-software|SOAPdenovo-Trans]]|1.03|'' | ||
|[[solexaqa-software|SolexaQA++]]|3.1.3|'' | |[[solexaqa-software|SolexaQA++]]|3.1.3|'' | ||
- | |[[spades-software|spades]]|3.11.1|'' | + | |[[spades-software|spades]]|3.15 (3.15.5)|'' |
|[[sourmash-software|sourmash]]|1.0|'' | |[[sourmash-software|sourmash]]|1.0|'' | ||
|[[speedseq-software|speedseq]]|0.1.2|'' | |[[speedseq-software|speedseq]]|0.1.2|'' | ||
|splitstree|4.11.3|'' | |splitstree|4.11.3|'' | ||
|spread|1.0.6|'' | |spread|1.0.6|'' | ||
- | |[[sratoolkit-software|sratoolkit]]|2.8.2|'' | + | |[[squid-software|squid]]|1.9g|'' |
+ | |[[sratoolkit-software|sratoolkit]]|2.10.0|'' | ||
+ | |[[sra-tools-software|sra-tools]]|3.0.0|'' | ||
+ | |[[srprism-software|srprism]]|3.1.2|'' | ||
|[[sspace-software|sspace]]|3.0|'' | |[[sspace-software|sspace]]|3.0|'' | ||
|[[sspace-longread-software|sspace-longread]]|1.1|'' | |[[sspace-longread-software|sspace-longread]]|1.1|'' | ||
- | |[[stacks-software|stacks]]|1.24|'' | + | |[[stacks-software|stacks]]|2.62|'' |
|staden|2.0.0b8|'' | |staden|2.0.0b8|'' | ||
- | |[[star-software|star]]|2.5.3a|'' | + | |[[star-software|star]]|2.7.10a|'' |
|[[structure-software|structure]]|2.3.4|'' | |[[structure-software|structure]]|2.3.4|'' | ||
|[[stringtie-software|stringtie]]|1.3.4d|'' | |[[stringtie-software|stringtie]]|1.3.4d|'' | ||
+ | |[[stringtie2-software|stringtie2]]|2.0.1|'' | ||
|[[subread-software|subread]]|1.6.2|'' | |[[subread-software|subread]]|1.6.2|'' | ||
|svmlight|V6.02|'' | |svmlight|V6.02|'' | ||
|tabix|git-76b4bbdf|'' | |tabix|git-76b4bbdf|'' | ||
|[[tablet-software|tablet]]|1.17.08.17|'' | |[[tablet-software|tablet]]|1.17.08.17|'' | ||
- | |[[tassel-software|tassel]]|4.0|'' | + | |[[tassel-software|tassel]]|5.2.77|'' |
|[[tmiseq-software|tmiseq]]|2016-01-31|'' | |[[tmiseq-software|tmiseq]]|2016-01-31|'' | ||
|[[tophat-software|tophat]]|2.1.0|'' | |[[tophat-software|tophat]]|2.1.0|'' | ||
|[[tracer-software|tracer]]|1.6|'' | |[[tracer-software|tracer]]|1.6|'' | ||
+ | |[[transabyss-software|transabyss]]|2.0.1|'' | ||
|[[transdecoder-software|TransDecoder]]|2.0.1|'' | |[[transdecoder-software|TransDecoder]]|2.0.1|'' | ||
|[[transrate-software|Transrate]]|1.0.3|'' | |[[transrate-software|Transrate]]|1.0.3|'' | ||
- | |[[trf-software|trf]]|4.0.4|'' | + | |[[trf-software|trf]]|4.0.9|'' |
- | |[[trimmomatic-software|trimmomatic]]|0.38|'' | + | |[[trimgalore-software|trimgalore]]|0.6.7|'' |
- | |[[trinity-software|trinity]]|v2.6.6|'' | + | |[[trimmomatic-software|trimmomatic]]|0.39|'' |
+ | |[[trinity-software|trinity]]|v2.11.0|'' | ||
|[[trinotate-software|trinotate]]|2.0.2|'' | |[[trinotate-software|trinotate]]|2.0.2|'' | ||
|[[twinscan-software|twinscan]]|3.5|'' | |[[twinscan-software|twinscan]]|3.5|'' | ||
- | |[[umi-tools-software|umi-tools]]| | + | |[[umi-tools-software|umi-tools]]| |
- | |[[usearch-software|usearch]]| | + | |[[unicycler-software|unicycler]]| 0.4.7 |'' |
+ | |[[usearch-software|usearch]]| | ||
|varscan|2.4.2|'' | |varscan|2.4.2|'' | ||
+ | |[[vcfdo-software|vcfdo]]|git-508cc19b|'' | ||
|[[vcflib-software|vcflib]]|git-7f1575e|'' | |[[vcflib-software|vcflib]]|git-7f1575e|'' | ||
- | |[[vcftools-software|vcftools]]|0.1.15|'' | + | |[[vcftools-software|vcftools]]|0.1.16|'' |
|[[velvet-software|velvet]]|1.2.10-kmer111|'' | |[[velvet-software|velvet]]|1.2.10-kmer111|'' | ||
+ | |[[velvetoptimiser-software|velvetoptimiser]]|2.2.6|'' | ||
|[[vep-software|vep]]|92.1|'' | |[[vep-software|vep]]|92.1|'' | ||
- | |[[vsearch-software|vsearch]]|2.8.0|'' | + | |[[vg-software|vg]]|1.27.0|'' |
+ | |[[viennarna-software|viennarna]]|2.4.14|'' | ||
|[[virusdetect-software|virusdetect]]|1.7|'' | |[[virusdetect-software|virusdetect]]|1.7|'' | ||
|[[vntrseek-software|vntrseek]]|1.08|'' | |[[vntrseek-software|vntrseek]]|1.08|'' | ||
+ | |[[vsearch-software|vsearch]]|2.8.0|'' | ||
|[[w2rap-software|w2rap]]|git-60781b6c|'' | |[[w2rap-software|w2rap]]|git-60781b6c|'' | ||
|[[w2rap-contigger-software|w2rap-contigger]]|git-a43f5a05|'' | |[[w2rap-contigger-software|w2rap-contigger]]|git-a43f5a05|'' | ||
|[[whatshap-software|whatshap]]|0.16|'' | |[[whatshap-software|whatshap]]|0.16|'' | ||
|[[wise-software|wise]]|2.4.1|'' | |[[wise-software|wise]]|2.4.1|'' | ||
+ | |[[wombat-software|wombat]]|2020-02-07|'' | ||
+ | |[[wtdbg2-software|wtdbg2]]|2.4|'' | ||
The source code for all environment modules can be found in [[https:// | The source code for all environment modules can be found in [[https:// |
list-of-software.txt · Last modified: 2024/09/24 07:20 by aorth