list-of-software
Differences
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list-of-software [2019/10/25 18:34] – aorth | list-of-software [2020/07/27 10:56] – aorth | ||
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|[[artemis-software|artemis]]|16.0.0|'' | |[[artemis-software|artemis]]|16.0.0|'' | ||
|[[augustus-software|augustus]]|3.3|'' | |[[augustus-software|augustus]]|3.3|'' | ||
+ | |[[awscli-software|awscli]]|1.17.9|'' | ||
|[[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|'' | ||
Line 36: | Line 37: | ||
|[[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]]|2.10.0+|'' |
|[[blobtools-software|blobtools]]|0.9.19.3|'' | |[[blobtools-software|blobtools]]|0.9.19.3|'' | ||
|blat|06-Aug-2013|'' | |blat|06-Aug-2013|'' | ||
- | |[[bowtie-software|bowtie1 ]]|1.1.1|'' | + | |[[bowtie-software|bowtie1 ]]|1.2.3|'' |
|[[bowtie2-software|bowtie2 ]]|2.3.4.1|'' | |[[bowtie2-software|bowtie2 ]]|2.3.4.1|'' | ||
|[[brig-software|brig]]|0.95|'' | |[[brig-software|brig]]|0.95|'' | ||
- | |[[busco-software|BUSCO ]]|3.0.2|'' | + | |[[busco-software|BUSCO ]]|4.0.6|'' |
- | |[[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|'' | ||
Line 52: | Line 53: | ||
|celera-wgs|6.1|'' | |celera-wgs|6.1|'' | ||
|censor|4.2.28|'' | |censor|4.2.28|'' | ||
- | |[[changeo-software|changeo]]|0.3.9|'' | + | |[[changeo-software|changeo]]|1.0.0|'' |
- | |[[circos-software|circos]]|0.67|'' | + | |[[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 67: | Line 69: | ||
|dendroscope|2.7.4|'' | |dendroscope|2.7.4|'' | ||
|[[diamond-software|diamond]]|0.9.9|'' | |[[diamond-software|diamond]]|0.9.9|'' | ||
+ | |[[drep-software|drep]]|2.5.4|'' | ||
|[[ea-utils-software|ea-utils]]|1.04.807|'' | |[[ea-utils-software|ea-utils]]|1.04.807|'' | ||
|[[edirect-software|edirect]]| 7.80 | '' | |[[edirect-software|edirect]]| 7.80 | '' | ||
Line 75: | Line 78: | ||
|[[exabayes-software|exabayes]]|1.4.1|'' | |[[exabayes-software|exabayes]]|1.4.1|'' | ||
|[[express-software|express]]|1.5.1|'' | |[[express-software|express]]|1.5.1|'' | ||
+ | |[[fastANI-software|fastANI]]|1.3|'' | ||
|[[fastPHASE-software|fastPHASE]]|1.4.8|'' | |[[fastPHASE-software|fastPHASE]]|1.4.8|'' | ||
|[[fastqc-software|fastqc]]|0.11.7|'' | |[[fastqc-software|fastqc]]|0.11.7|'' | ||
|[[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 87: | Line 92: | ||
|[[flye-software|flye]]|2.4.2|'' | |[[flye-software|flye]]|2.4.2|'' | ||
|frappe|1.1|'' | |frappe|1.1|'' | ||
- | |[[fraggenescan-software|FragGeneScan ]]|1.19|'' | + | |[[fraggenescan-software|FragGeneScan ]]|1.30|'' |
|[[freebayes-software|FreeBayes ]]|1.0.2|'' | |[[freebayes-software|FreeBayes ]]|1.0.2|'' | ||
|[[gassflow-software|GassFlow ]]|1.0|'' | |[[gassflow-software|GassFlow ]]|1.0|'' | ||
Line 103: | Line 108: | ||
|[[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|'' | ||
|[[hapflk-software|hapflk]]|1.4|'' | |[[hapflk-software|hapflk]]|1.4|'' | ||
|hapmix|2.0|'' | |hapmix|2.0|'' | ||
|[[hdf5-software|hdf5]]|1.8.19|'' | |[[hdf5-software|hdf5]]|1.8.19|'' | ||
- | |[[hmmer-software|hmmer]]|3.1b2|'' | + | |[[hmmer-software|hmmer]]|3.3|'' |
|[[hpg-variant-software|hpg-variant]]|1.0|'' | |[[hpg-variant-software|hpg-variant]]|1.0|'' | ||
|[[hisat2-software|hisat2]]|2.1.0|'' | |[[hisat2-software|hisat2]]|2.1.0|'' | ||
|[[htseq-software|htseq]]|0.9.1|'' | |[[htseq-software|htseq]]|0.9.1|'' | ||
|[[htslib-software|htslib]]|1.9|'' | |[[htslib-software|htslib]]|1.9|'' | ||
- | |[[igblast-software|igblast]]|1.6.0|'' | + | |[[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|'' | ||
|[[igv-software|igv]]|2.4.5|'' | |[[igv-software|igv]]|2.4.5|'' | ||
|[[igvtools-software|igvtools]]|2.3.98|'' | |[[igvtools-software|igvtools]]|2.3.98|'' | ||
Line 142: | Line 151: | ||
|[[marginalign-software|marginalign]]|git-2369dafd|'' | |[[marginalign-software|marginalign]]|git-2369dafd|'' | ||
|[[marginpolish-software|marginpolish]]|1.0.0|'' | |[[marginpolish-software|marginpolish]]|1.0.0|'' | ||
- | |[[mash-software|mash]]|2.0|'' | + | |[[mash-software|mash]]|2.2|'' |
|[[masurca-software|masurca]]|3.3.1|'' | |[[masurca-software|masurca]]|3.3.1|'' | ||
|mauve|2.3.1|'' | |mauve|2.3.1|'' | ||
+ | |[[maxbin2-software|maxbin2]]|2.2.7|'' | ||
|maximus|0.2|'' | |maximus|0.2|'' | ||
|[[mcl-software|mcl]]|14-137|'' | |[[mcl-software|mcl]]|14-137|'' | ||
Line 153: | Line 163: | ||
|[[megax-software|megax]]|10.0.5|'' | |[[megax-software|megax]]|10.0.5|'' | ||
|[[metabat-software|metabat]]|2.12.1|'' | |[[metabat-software|metabat]]|2.12.1|'' | ||
+ | |[[metaphlan2-software|metaphlan2]]|2.9.5|'' | ||
|[[metis-software|metis]]|5.1.0|'' | |[[metis-software|metis]]|5.1.0|'' | ||
|[[migec-software|migec]]|1.2.4a|'' | |[[migec-software|migec]]|1.2.4a|'' | ||
Line 159: | Line 170: | ||
|[[minimap2-software|minimap2]]|2.13|'' | |[[minimap2-software|minimap2]]|2.13|'' | ||
|[[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|'' | + | |[[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]]|1.4|'' | ||
- | |[[muscle-software|muscle]]|3.8.31|'' | + | |[[muscle-software|muscle]]|3.8.1551|'' |
|[[mummer-software|MUMmer]]|3.23|'' | |[[mummer-software|MUMmer]]|3.23|'' | ||
|[[nanopolish-software|nanopolish]]|0.10.2|'' | |[[nanopolish-software|nanopolish]]|0.10.2|'' | ||
|[[netmhcpan-software|netmhcpan]]|2.8|'' | |[[netmhcpan-software|netmhcpan]]|2.8|'' | ||
|[[nextclip-software|nextclip]]|1.3.1|'' | |[[nextclip-software|nextclip]]|1.3.1|'' | ||
+ | |[[nextflow-software|nextflow]]|20.04.1|'' | ||
|[[ntcard-software|ntCard]]|1.0.0|'' | |[[ntcard-software|ntCard]]|1.0.0|'' | ||
|[[ngsqctoolkit-software|ngsqctoolkit]]|2.3.3|'' | |[[ngsqctoolkit-software|ngsqctoolkit]]|2.3.3|'' | ||
Line 187: | Line 200: | ||
|[[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|'' | + | |[[pear-software|pear]]|0.9.6|'' |
|[[pblat-software|pblat]]|2.1|'' | |[[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 200: | Line 213: | ||
|[[pilon-software|pilon]]|1.23|'' | |[[pilon-software|pilon]]|1.23|'' | ||
|[[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|'' | ||
+ | |[[porechop-software|porechop]]|0.2.4|'' | ||
+ | |[[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|'' |
|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]]|3.7.2|'' | + | |[[python-software|python]]|3.7.7|'' |
|qdd|3_beta|'' | |qdd|3_beta|'' | ||
|[[qiime-software|qiime]]|1.9.1|'' | |[[qiime-software|qiime]]|1.9.1|'' | ||
- | |[[qiime2-software|qiime2]]|2019.7|'' | + | |[[qiime2-software|qiime2]]|2019.10|'' |
- | |[[quast-software|quast]]|4.5|'' | + | |[[quast-software|quast]]|5.0.2|'' |
|[[quickmerge-software|quickmerge]]|0.3|'' | |[[quickmerge-software|quickmerge]]|0.3|'' | ||
|[[quorum-software|Quorum]]|1.1.1|'' | |[[quorum-software|Quorum]]|1.1.1|'' | ||
Line 217: | Line 234: | ||
|[[racon-software|racon]]|1.3.1|'' | |[[racon-software|racon]]|1.3.1|'' | ||
|[[rmblast-software|rmblast]]|2.2.28|'' | |[[rmblast-software|rmblast]]|2.2.28|'' | ||
- | |rapsearch|2.10|'' | + | |[[rapsearch-software|rapsearch]]|2.22|'' |
|[[ratt-software|RATT]]|r18|'' | |[[ratt-software|RATT]]|r18|'' | ||
|[[raxml-software|RAxML]]|8.2.12|'' | |[[raxml-software|RAxML]]|8.2.12|'' | ||
Line 223: | Line 240: | ||
|[[rdp-classifier-software|RDP Classifier]]|2.11|'' | |[[rdp-classifier-software|RDP Classifier]]|2.11|'' | ||
|repeatmasker|4.0.5|'' | |repeatmasker|4.0.5|'' | ||
+ | |[[repseqio-software|repseqio]]|1.3.3|'' | ||
|[[root-software|root]]|6.08.06|'' | |[[root-software|root]]|6.08.06|'' | ||
|[[rrnaselector-software|rRNASelector]]|1.1|'' | |[[rrnaselector-software|rRNASelector]]|1.1|'' | ||
Line 233: | Line 251: | ||
|[[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]]|4.3.8|'' | ||
|[[seroba-software|seroba]]|1.0.0|'' | |[[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]]|1.3|'' | |[[seqtk-software|seqtk]]|1.3|'' | ||
|[[shannon-software|shannon]]|0.0.2|'' | |[[shannon-software|shannon]]|0.0.2|'' | ||
- | |[[shasta-software|shasta]]|0.2.0|'' | + | |[[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|'' | ||
Line 261: | Line 280: | ||
|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|'' | ||
|[[sspace-software|sspace]]|3.0|'' | |[[sspace-software|sspace]]|3.0|'' | ||
|[[sspace-longread-software|sspace-longread]]|1.1|'' | |[[sspace-longread-software|sspace-longread]]|1.1|'' | ||
Line 292: | Line 312: | ||
|[[velvet-software|velvet]]|1.2.10-kmer111|'' | |[[velvet-software|velvet]]|1.2.10-kmer111|'' | ||
|[[vep-software|vep]]|92.1|'' | |[[vep-software|vep]]|92.1|'' | ||
- | |[[vsearch-software|vsearch]]|2.8.0|'' | + | |[[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|'' | |[[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