list-of-software
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list-of-software [2020/09/15 12:56] – aorth | list-of-software [2021/02/14 10:44] – aorth | ||
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|[[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|'' | ||
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|[[exabayes-software|exabayes]]|1.4.1|'' | |[[exabayes-software|exabayes]]|1.4.1|'' | ||
|[[express-software|express]]|1.5.1|'' | |[[express-software|express]]|1.5.1|'' | ||
+ | |[[falcon-phase-software|falcon-phase]]|git-7c50154e|'' | ||
|[[fastANI-software|fastANI]]|1.3|'' | |[[fastANI-software|fastANI]]|1.3|'' | ||
|[[fastPHASE-software|fastPHASE]]|1.4.8|'' | |[[fastPHASE-software|fastPHASE]]|1.4.8|'' | ||
Line 92: | Line 94: | ||
|[[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]]|2.4.2|'' | + | |[[flye-software|flye]]|2.8.1|'' |
|frappe|1.1|'' | |frappe|1.1|'' | ||
|[[fraggenescan-software|FragGeneScan ]]|1.30|'' | |[[fraggenescan-software|FragGeneScan ]]|1.30|'' | ||
Line 100: | Line 102: | ||
|[[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|'' | ||
|[[genscan-software|genscan]]|latest|'' | |[[genscan-software|genscan]]|latest|'' | ||
|[[gffread-software|gffread]]|0.9.6|'' | |[[gffread-software|gffread]]|0.9.6|'' | ||
Line 117: | Line 120: | ||
|[[hmmer-software|hmmer]]|3.3|'' | |[[hmmer-software|hmmer]]|3.3|'' | ||
|[[hpg-variant-software|hpg-variant]]|1.0|'' | |[[hpg-variant-software|hpg-variant]]|1.0|'' | ||
+ | |[[hic_qc-software|hic_qc]]|git-1e132fb2|'' | ||
|[[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]]|1.11|'' |
+ | |[[hypo-software|hypo]]|1.0.3|'' | ||
|[[idba-software|idba]]|1.1.2|'' | |[[idba-software|idba]]|1.1.2|'' | ||
|[[igblast-software|igblast]]|1.10.0|'' | |[[igblast-software|igblast]]|1.10.0|'' | ||
Line 131: | Line 136: | ||
|[[interproscan-software|interproscan]]|5.13|'' | |[[interproscan-software|interproscan]]|5.13|'' | ||
|i-tasser|latest|'' | |i-tasser|latest|'' | ||
- | |[[jellyfish-software|jellyfish]]|2.2.9|'' | + | |[[ivar-software|ivar]]|1.3|'' |
+ | |[[jellyfish-software|jellyfish]]|2.3.0|'' | ||
|jMHC|1.5.0929|'' | |jMHC|1.5.0929|'' | ||
- | |julia|v0.1.2|'' | + | |[[juicebox-software|juicebox]]|1.11.08|'' |
+ | |[[juicer-software|juicer]]|1.6|'' | ||
|[[kaiju-software|kaiju]]|1.4.4|'' | |[[kaiju-software|kaiju]]|1.4.4|'' | ||
|[[kallisto-software|kallisto]]|0.43.0|'' | |[[kallisto-software|kallisto]]|0.43.0|'' | ||
|[[karect-software|karect]]|1.0|'' | |[[karect-software|karect]]|1.0|'' | ||
|[[kat-software|kat]]|2.3.4|'' | |[[kat-software|kat]]|2.3.4|'' | ||
- | |[[kmc-software|kmc]]|3.0.0|'' | + | |[[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|'' | ||
Line 151: | Line 158: | ||
|lucy|1.19p|'' | |lucy|1.19p|'' | ||
|[[mafft-software|mafft]]|7.313|'' | |[[mafft-software|mafft]]|7.313|'' | ||
+ | |[[maker-software|maker]]|3.01.03|'' | ||
|[[mapsplice-software|mapsplice]]|2.2.0|'' | |[[mapsplice-software|mapsplice]]|2.2.0|'' | ||
|[[marginalign-software|marginalign]]|git-2369dafd|'' | |[[marginalign-software|marginalign]]|git-2369dafd|'' | ||
Line 186: | Line 194: | ||
|[[multiqc-software|multiqc]]|1.6|'' | |[[multiqc-software|multiqc]]|1.6|'' | ||
|[[muscle-software|muscle]]|3.8.1551|'' | |[[muscle-software|muscle]]|3.8.1551|'' | ||
- | |[[mummer-software|MUMmer]]|3.23|'' | + | |[[mummer-software|mummer]]|4.0.0rc1|'' |
|[[nanopolish-software|nanopolish]]|0.10.2|'' | |[[nanopolish-software|nanopolish]]|0.10.2|'' | ||
|[[netmhcpan-software|netmhcpan]]|2.8|'' | |[[netmhcpan-software|netmhcpan]]|2.8|'' | ||
+ | |[[nextclade-software|nextclade]]|0.12.0|'' | ||
|[[nextclip-software|nextclip]]|1.3.1|'' | |[[nextclip-software|nextclip]]|1.3.1|'' | ||
|[[nextflow-software|nextflow]]|20.04.1|'' | |[[nextflow-software|nextflow]]|20.04.1|'' | ||
Line 217: | Line 226: | ||
|[[picrust-software# | |[[picrust-software# | ||
|[[pilon-software|pilon]]|1.23|'' | |[[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]]|2.00-alpha|'' | |[[plink-software|plink]]|2.00-alpha|'' | ||
Line 232: | Line 242: | ||
|qdd|3_beta|'' | |qdd|3_beta|'' | ||
|[[qiime-software|qiime]]|1.9.1|'' | |[[qiime-software|qiime]]|1.9.1|'' | ||
- | |[[qiime2-software|qiime2]]|2019.10|'' | + | |[[qiime2-software|qiime2]]|2020.8|'' |
|[[quast-software|quast]]|5.0.2|'' | |[[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|'' | ||
- | |[[r-software|R]]|3.6.1|'' | + | |[[r-software|R]]|4.0.3|'' |
|[[racon-software|racon]]|1.3.1|'' | |[[racon-software|racon]]|1.3.1|'' | ||
- | |[[rmblast-software|rmblast]]|2.2.28|'' | + | |[[rmblast-software|rmblast]]|2.10.0|'' |
|[[rapsearch-software|rapsearch]]|2.22|'' | |[[rapsearch-software|rapsearch]]|2.22|'' | ||
|[[ratt-software|RATT]]|r18|'' | |[[ratt-software|RATT]]|r18|'' | ||
Line 244: | Line 254: | ||
|[[ray-software|ray]]|2.3.1|'' | |[[ray-software|ray]]|2.3.1|'' | ||
|[[rdp-classifier-software|RDP Classifier]]|2.11|'' | |[[rdp-classifier-software|RDP Classifier]]|2.11|'' | ||
- | |repeatmasker|4.0.5|'' | + | |[[repeatmasker-software|repeatmasker]]|4.1.1|'' |
|[[repseqio-software|repseqio]]|1.3.3|'' | |[[repseqio-software|repseqio]]|1.3.3|'' | ||
|[[root-software|root]]|6.08.06|'' | |[[root-software|root]]|6.08.06|'' | ||
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|[[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]]|1.9|'' | + | |[[samtools-software|samtools]]|1.11|'' |
|[[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|'' | ||
|[[scipio-software|scipio]]|1.4.1|'' | |[[scipio-software|scipio]]|1.4.1|'' | ||
|[[scythe-software|scythe]]|0.994-beta|'' | |[[scythe-software|scythe]]|0.994-beta|'' | ||
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|[[seqqs-software|seqqs]]|git-3d053750|'' | |[[seqqs-software|seqqs]]|git-3d053750|'' | ||
|[[seqtk-software|seqtk]]|1.3|'' | |[[seqtk-software|seqtk]]|1.3|'' | ||
+ | |[[seqwish-software|seqwish]]|0.6|'' | ||
|[[shannon-software|shannon]]|0.0.2|'' | |[[shannon-software|shannon]]|0.0.2|'' | ||
|[[shasta-software|shasta]]|0.4.0|'' | |[[shasta-software|shasta]]|0.4.0|'' | ||
Line 305: | Line 317: | ||
|[[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|'' | |[[trimmomatic-software|trimmomatic]]|0.38|'' | ||
- | |[[trinity-software|trinity]]|v2.6.6|'' | + | |[[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|'' | ||
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|[[velvet-software|velvet]]|1.2.10-kmer111|'' | |[[velvet-software|velvet]]|1.2.10-kmer111|'' | ||
|[[vep-software|vep]]|92.1|'' | |[[vep-software|vep]]|92.1|'' | ||
+ | |[[vg-software|vg]]|1.27.0|'' | ||
|[[viennarna-software|viennarna]]|2.4.14|'' | |[[viennarna-software|viennarna]]|2.4.14|'' | ||
|[[virusdetect-software|virusdetect]]|1.7|'' | |[[virusdetect-software|virusdetect]]|1.7|'' |
list-of-software.txt · Last modified: 2024/06/19 11:50 by aorth