list-of-software
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list-of-software [2023/02/14 11:28] – aorth | list-of-software [2023/09/05 07:21] – aorth | ||
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|[[angsd-software|angsd]]|0.910|'' | |[[angsd-software|angsd]]|0.910|'' | ||
|[[annovar-software|annovar]]|2016-02-01|'' | |[[annovar-software|annovar]]|2016-02-01|'' | ||
+ | |[[antismash-software|antismash]]|7.0.0|'' | ||
|[[any2fasta-software|any2fasta]]|0.4.2|'' | |[[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-software|artic]]|1.2.3|'' | ||
+ | |[[artic-tools-software|artic-tools]]|0.3.1|'' | ||
|[[augustus-software|augustus]]|3.3|'' | |[[augustus-software|augustus]]|3.3|'' | ||
|[[awscli-software|awscli]]|2.4.0|'' | |[[awscli-software|awscli]]|2.4.0|'' | ||
Line 30: | Line 33: | ||
|bayescan|2.1|'' | |bayescan|2.1|'' | ||
|[[bbmap-software|bbmap]]|38.95|'' | |[[bbmap-software|bbmap]]|38.95|'' | ||
- | |[[bcftools-software|bcftools]]|1.13|'' | + | |[[bcftools-software|bcftools]]|1.15.1|'' |
|bcl2fastq|2.20.0.422|'' | |bcl2fastq|2.20.0.422|'' | ||
|[[beagle-software|beagle]]|3.1.2|'' | |[[beagle-software|beagle]]|3.1.2|'' | ||
Line 99: | Line 102: | ||
|[[fasttree-software|fasttree]]|2.1.11|'' | |[[fasttree-software|fasttree]]|2.1.11|'' | ||
|[[fastx-toolkit-software|fastx_toolkit]]|0.0.13|'' | |[[fastx-toolkit-software|fastx_toolkit]]|0.0.13|'' | ||
+ | |[[figaro-software|figaro]]|git-337aa9|'' | ||
|figtree|1.4.0|'' | |figtree|1.4.0|'' | ||
|[[flapjack-software|flapjack ]]|1.18.04.23-beta|'' | |[[flapjack-software|flapjack ]]|1.18.04.23-beta|'' | ||
Line 109: | Line 113: | ||
|[[fraggenescan-software|FragGeneScan ]]|1.30|'' | |[[fraggenescan-software|FragGeneScan ]]|1.30|'' | ||
|[[freebayes-software|freebayes]]|1.3.4|'' | |[[freebayes-software|freebayes]]|1.3.4|'' | ||
- | |[[funannotate-software|funannotate]]|1.8.11|See software page| | | + | |[[funannotate-software|funannotate]]|1.8.15|See software page| | |
|[[gassflow-software|GassFlow ]]|1.0|'' | |[[gassflow-software|GassFlow ]]|1.0|'' | ||
- | |[[gatk-software|gatk]]|4.3.0.0|'' | + | |[[gatk-software|gatk]]|4.4.0.0|'' |
|[[gapfiller-software|gapfiller]]|1.10|'' | |[[gapfiller-software|gapfiller]]|1.10|'' | ||
|[[geneid-software|geneid]]|1.4.4|'' | |[[geneid-software|geneid]]|1.4.4|'' | ||
Line 145: | Line 149: | ||
|[[htslib-software|htslib]]|1.15.1|'' | |[[htslib-software|htslib]]|1.15.1|'' | ||
|[[hypo-software|hypo]]|1.0.3|'' | |[[hypo-software|hypo]]|1.0.3|'' | ||
+ | |[[hyphy-software|hyphy]]|2.5.48|'' | ||
|[[idba-software|idba]]|1.1.2|'' | |[[idba-software|idba]]|1.1.2|'' | ||
|[[igblast-software|igblast]]|1.10.0|'' | |[[igblast-software|igblast]]|1.10.0|'' | ||
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|[[kma-software|kma]]|1.4.11|'' | |[[kma-software|kma]]|1.4.11|'' | ||
|[[kmc-software|kmc]]|3.1.1|'' | |[[kmc-software|kmc]]|3.1.1|'' | ||
+ | |[[kmerfreq-software|kmerfreq]]|git-90fca00d|'' | ||
|[[kmergenie-software|kmergenie]]|1.7038|'' | |[[kmergenie-software|kmergenie]]|1.7038|'' | ||
|[[kmer-ssr-software|kmer-ssr]]|git-4043c0e7|'' | |[[kmer-ssr-software|kmer-ssr]]|git-4043c0e7|'' | ||
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|[[libsvm-software|libsvm]]|3.20|'' | |[[libsvm-software|libsvm]]|3.20|'' | ||
|[[lighter-software|lighter]]|1.1.2|'' | |[[lighter-software|lighter]]|1.1.2|'' | ||
+ | |[[longshot-software|longshot]]|0.4.5|'' | ||
|[[lordec-software|lordec]]|0.9|'' | |[[lordec-software|lordec]]|0.9|'' | ||
|[[ltr_retriever-software|ltr_retriever]]|2.9.0|'' | |[[ltr_retriever-software|ltr_retriever]]|2.9.0|'' | ||
Line 185: | Line 192: | ||
|[[marginpolish-software|marginpolish]]|1.0.0|'' | |[[marginpolish-software|marginpolish]]|1.0.0|'' | ||
|[[mash-software|mash]]|2.2|'' | |[[mash-software|mash]]|2.2|'' | ||
- | |[[masurca-software|masurca]]|3.3.1|'' | + | |[[masurca-software|masurca]]|4.1.0|'' |
|mauve|2.3.1|'' | |mauve|2.3.1|'' | ||
|[[maxbin2-software|maxbin2]]|2.2.7|'' | |[[maxbin2-software|maxbin2]]|2.2.7|'' | ||
Line 198: | Line 205: | ||
|[[metabat-software|metabat]]|2.12.1|'' | |[[metabat-software|metabat]]|2.12.1|'' | ||
|[[metaeuk-software|metaeuk]]|git-9818d1a5|'' | |[[metaeuk-software|metaeuk]]|git-9818d1a5|'' | ||
- | |[[metaphlan-software|metaphlan]]|3.0.13|'' | + | |[[metaphlan-software|metaphlan]]|4.0.6|'' |
|[[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 205: | Line 212: | ||
|[[minimac3-software|minimac3]]|2.0.1|'' | |[[minimac3-software|minimac3]]|2.0.1|'' | ||
|[[minimac4-software|minimac4]]|1.0.3|'' | |[[minimac4-software|minimac4]]|1.0.3|'' | ||
- | |[[minimap2-software|minimap2]]|2.22|'' | + | |[[minimap2-software|minimap2]]|2.24|'' |
|[[minpath-software|MinPath]]|1.0.2|'' | |[[minpath-software|MinPath]]|1.0.2|'' | ||
|[[mira-software# | |[[mira-software# | ||
Line 221: | Line 228: | ||
|[[muscle-software|muscle]]|3.8.1551|'' | |[[muscle-software|muscle]]|3.8.1551|'' | ||
|[[mummer-software|mummer]]|4.0.0rc1|'' | |[[mummer-software|mummer]]|4.0.0rc1|'' | ||
- | |[[nanopolish-software|nanopolish]]|0.10.2|'' | + | |[[nanopolish-software|nanopolish]]|0.14.0|'' |
|[[netmhcpan-software|netmhcpan]]|2.8|'' | |[[netmhcpan-software|netmhcpan]]|2.8|'' | ||
|[[nextalign-software|nextalign]]|1.11.0|'' | |[[nextalign-software|nextalign]]|1.11.0|'' | ||
- | |[[nextclade-software|nextclade]]|1.11.0|'' | + | |[[nextclade-software|nextclade]]|2.11.0|'' |
|[[nextclip-software|nextclip]]|1.3.1|'' | |[[nextclip-software|nextclip]]|1.3.1|'' | ||
- | |[[nextflow-software|nextflow]]|21.10 (21.10.6)|'' | + | |[[nextflow-software|nextflow]]|23.04 (23.04.2)|'' |
|[[ngs-tools-software|ngs-tools]]|3.0.0|'' | |[[ngs-tools-software|ngs-tools]]|3.0.0|'' | ||
|[[ntcard-software|ntCard]]|1.0.0|'' | |[[ntcard-software|ntCard]]|1.0.0|'' | ||
Line 243: | Line 250: | ||
|[[pairfq-software|pairfq]]|0.14.4|'' | |[[pairfq-software|pairfq]]|0.14.4|'' | ||
|[[paml-software|paml]]|4.9a|'' | |[[paml-software|paml]]|4.9a|'' | ||
+ | |[[panaroo-software|panaroo]]|1.3.3|'' | ||
|[[pandaseq-software|pandaseq]]|2.8.1|'' | |[[pandaseq-software|pandaseq]]|2.8.1|'' | ||
|[[pasta-software|pasta]]|d939adb2|'' | |[[pasta-software|pasta]]|d939adb2|'' | ||
Line 258: | Line 266: | ||
|[[picrust-software# | |[[picrust-software# | ||
|[[pilon-software|pilon]]|1.23|'' | |[[pilon-software|pilon]]|1.23|'' | ||
- | |[[plasmidid-software|plasmidid]]|1.6.3|'' | + | |[[plasmidid-software|plasmidid]]|1.6.5|'' |
|[[platanus-software|platanus]]|1.2.1|'' | |[[platanus-software|platanus]]|1.2.1|'' | ||
|[[plink-software|plink]]|2.00-alpha|'' | |[[plink-software|plink]]|2.00-alpha|'' | ||
|[[polyphen-software|polyphen]]|2.2.2|'' | |[[polyphen-software|polyphen]]|2.2.2|'' | ||
|[[poplddecay-software|poplddecay]]|3.41|'' | |[[poplddecay-software|poplddecay]]|3.41|'' | ||
- | |[[porechop-software|porechop]]|0.2.4|'' | + | |[[porechop-software|porechop]]|0.3.2pre|'' |
|[[pplacer-software|pplacer]]|1.1.alpha19|'' | |[[pplacer-software|pplacer]]|1.1.alpha19|'' | ||
|[[prank-software|prank]]|170427|'' | |[[prank-software|prank]]|170427|'' | ||
Line 274: | Line 282: | ||
|[[provean-software|provean]]|1.1.5|'' | |[[provean-software|provean]]|1.1.5|'' | ||
|[[purge-haplotigs-software|purge_haplotigs]]|1.1.1|'' | |[[purge-haplotigs-software|purge_haplotigs]]|1.1.1|'' | ||
- | |[[python-software|python]]|3.9.14|'' | + | |[[python-software|python]]|3.9.17|'' |
|qdd|3_beta|'' | |qdd|3_beta|'' | ||
|[[qiime-software|qiime]]|1.9.1|'' | |[[qiime-software|qiime]]|1.9.1|'' | ||
Line 281: | Line 289: | ||
|[[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]]|4.2.0|'' | + | |[[r-software|R]]|4.3.1|'' |
- | |[[racon-software|racon]]|1.3.1|'' | + | |[[racon-software|racon]]|1.5.0|'' |
|[[rapsearch-software|rapsearch]]|2.22|'' | |[[rapsearch-software|rapsearch]]|2.22|'' | ||
|[[ratt-software|RATT]]|r18|'' | |[[ratt-software|RATT]]|r18|'' | ||
Line 316: | Line 324: | ||
|[[shannon-software|shannon]]|0.0.2|'' | |[[shannon-software|shannon]]|0.0.2|'' | ||
|[[shannon_cpp-software|shannon_cpp]]|0.5.0|'' | |[[shannon_cpp-software|shannon_cpp]]|0.5.0|'' | ||
+ | |[[shapeit-software|shapeit]]|2.904|'' | ||
|[[shasta-software|shasta]]|0.4.0|'' | |[[shasta-software|shasta]]|0.4.0|'' | ||
|[[sickle-software|sickle]]|1.33|'' | |[[sickle-software|sickle]]|1.33|'' | ||
Line 324: | Line 333: | ||
|[[snakemake-software|snakemake]]|6.15.5|'' | |[[snakemake-software|snakemake]]|6.15.5|'' | ||
|[[sniffles-software|sniffles]]|1.0.12b|'' | |[[sniffles-software|sniffles]]|1.0.12b|'' | ||
+ | |[[snippy-software|snippy]]|4.6.0|'' | ||
|snowhite|1.1.4|'' | |snowhite|1.1.4|'' | ||
- | |[[snpeff-software|SnpEff & SnpSift]]|4.1g|'' | + | |[[snpeff-software|snpeff]]|5.1|'' |
|[[snpmeta-software|snpmeta]]|2.0|'' | |[[snpmeta-software|snpmeta]]|2.0|'' | ||
|[[snp-pipeline-software|snp-pipeline]]|1.0.1|'' | |[[snp-pipeline-software|snp-pipeline]]|1.0.1|'' | ||
Line 343: | Line 353: | ||
|[[sra-tools-software|sra-tools]]|3.0.0|'' | |[[sra-tools-software|sra-tools]]|3.0.0|'' | ||
|[[srprism-software|srprism]]|3.1.2|'' | |[[srprism-software|srprism]]|3.1.2|'' | ||
+ | |[[srst2-software|srst2]]|git-73f885f5|'' | ||
|[[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 369: | Line 380: | ||
|[[twinscan-software|twinscan]]|3.5|'' | |[[twinscan-software|twinscan]]|3.5|'' | ||
|[[umi-tools-software|umi-tools]]| 0.2.3 |'' | |[[umi-tools-software|umi-tools]]| 0.2.3 |'' | ||
- | |[[unicycler-software|unicycler]]| 0.4.7 |'' | + | |[[unicycler-software|unicycler]]| 0.4.0 |'' |
|[[usearch-software|usearch]]| v7.0.1090 |'' | |[[usearch-software|usearch]]| v7.0.1090 |'' | ||
|varscan|2.4.2|'' | |varscan|2.4.2|'' | ||
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|[[velvet-software|velvet]]|1.2.10-kmer111|'' | |[[velvet-software|velvet]]|1.2.10-kmer111|'' | ||
|[[velvetoptimiser-software|velvetoptimiser]]|2.2.6|'' | |[[velvetoptimiser-software|velvetoptimiser]]|2.2.6|'' | ||
- | |[[vep-software|vep]]|92.1|'' | + | |[[vep-software|vep]]|109.3|'' |
|[[vg-software|vg]]|1.27.0|'' | |[[vg-software|vg]]|1.27.0|'' | ||
|[[viennarna-software|viennarna]]|2.4.14|'' | |[[viennarna-software|viennarna]]|2.4.14|'' |
list-of-software.txt · Last modified: 2024/06/19 11:50 by aorth