list-of-software
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list-of-software [2023/05/22 06:11] – aorth | list-of-software [2023/12/18 06:49] – aorth | ||
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|[[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]]|2.12.0+|'' | + | |[[blast-software|blast]]|2.14.1+|'' |
|[[blobtools-software|blobtools]]|0.9.19.3|'' | |[[blobtools-software|blobtools]]|0.9.19.3|'' | ||
|[[blat-software|blat]]|37x1|'' | |[[blat-software|blat]]|37x1|'' | ||
Line 60: | Line 60: | ||
|[[cd-hit-software|cd-hit]]|4.8.1|'' | |[[cd-hit-software|cd-hit]]|4.8.1|'' | ||
|[[cegma-software|cegma]]|v2.5|'' | |[[cegma-software|cegma]]|v2.5|'' | ||
+ | |[[cgmlst-dists-software|cgmlst-dists]]|0.4.0|'' | ||
|celera-wgs|6.1|'' | |celera-wgs|6.1|'' | ||
|censor|4.2.28|'' | |censor|4.2.28|'' | ||
Line 65: | Line 66: | ||
|[[changeo-software|changeo]]|1.2.0|'' | |[[changeo-software|changeo]]|1.2.0|'' | ||
|[[checkm-software|checkm]]|1.1.2|'' | |[[checkm-software|checkm]]|1.1.2|'' | ||
+ | |[[chewbbaca-software|chewbbaca]]|git-87102063|'' | ||
|[[circos-software|circos]]|0.69-9|'' | |[[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|'' | ||
- | |[[clustalo-software|clustalo]]|1.2.3|'' | ||
|clustalw|2.1|'' | |clustalw|2.1|'' | ||
|[[cnvnator-software|CNVnator]]|0.3.3|'' | |[[cnvnator-software|CNVnator]]|0.3.3|'' | ||
Line 81: | Line 82: | ||
|dendroscope|2.7.4|'' | |dendroscope|2.7.4|'' | ||
|[[diamond-software|diamond]]|2.0.14|'' | |[[diamond-software|diamond]]|2.0.14|'' | ||
+ | |[[disty-software|disty]]|0.1.0|'' | ||
+ | |[[dorado-software|dorado]]|0.5.0|'' | ||
|[[drep-software|drep]]|2.5.4|'' | |[[drep-software|drep]]|2.5.4|'' | ||
|[[ea-utils-software|ea-utils]]|1.04.807|'' | |[[ea-utils-software|ea-utils]]|1.04.807|'' | ||
Line 102: | Line 105: | ||
|[[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 158: | Line 162: | ||
|[[igvtools-software|igvtools]]|2.3.98|'' | |[[igvtools-software|igvtools]]|2.3.98|'' | ||
|[[infernal-software|infernal]]|1.1.2|'' | |[[infernal-software|infernal]]|1.1.2|'' | ||
+ | |[[integron-finder-software|integron-finder]]|2.0.2|'' | ||
|[[interproscan-software|interproscan]]|5.13|'' | |[[interproscan-software|interproscan]]|5.13|'' | ||
|i-tasser|latest|'' | |i-tasser|latest|'' | ||
Line 171: | Line 176: | ||
|[[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|'' | ||
Line 184: | Line 190: | ||
|[[ltr_retriever-software|ltr_retriever]]|2.9.0|'' | |[[ltr_retriever-software|ltr_retriever]]|2.9.0|'' | ||
|lucy|1.19p|'' | |lucy|1.19p|'' | ||
- | |[[mafft-software|mafft]]|7.475|'' | + | |[[mafft-software|mafft]]|7.505|'' |
|[[maker-software|maker]]|3.01.03|'' | |[[maker-software|maker]]|3.01.03|'' | ||
|[[mapsplice-software|mapsplice]]|2.2.0|'' | |[[mapsplice-software|mapsplice]]|2.2.0|'' | ||
Line 190: | Line 196: | ||
|[[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 203: | Line 209: | ||
|[[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 222: | Line 228: | ||
|[[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-software|mrbayes]]|3.2.7a|'' |
|[[multiqc-software|multiqc]]|1.12|'' | |[[multiqc-software|multiqc]]|1.12|'' | ||
|[[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]]|0.14.0|'' | |[[nanopolish-software|nanopolish]]|0.14.0|'' | ||
+ | |[[nanoqc-software|nanoqc]]|git-a7bcbdce|'' | ||
|[[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]]|2.11.0|'' | |[[nextclade-software|nextclade]]|2.11.0|'' | ||
|[[nextclip-software|nextclip]]|1.3.1|'' | |[[nextclip-software|nextclip]]|1.3.1|'' | ||
- | |[[nextflow-software|nextflow]]|22.10 (22.10.8)|'' | + | |[[nextflow-software|nextflow]]|23.10 (23.10.0)|'' |
|[[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 237: | Line 244: | ||
|[[ngsqctoolkit-software|ngsqctoolkit]]|2.3.3|'' | |[[ngsqctoolkit-software|ngsqctoolkit]]|2.3.3|'' | ||
|[[nQuire-software|nQuire]]|git-a990a88e|'' | |[[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|'' | ||
Line 248: | Line 254: | ||
|[[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 263: | Line 270: | ||
|[[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|'' | ||
+ | |[[pod5-software|pod5]]|0.3.2|'' | ||
|[[polyphen-software|polyphen]]|2.2.2|'' | |[[polyphen-software|polyphen]]|2.2.2|'' | ||
|[[poplddecay-software|poplddecay]]|3.41|'' | |[[poplddecay-software|poplddecay]]|3.41|'' | ||
Line 279: | Line 287: | ||
|[[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 286: | Line 294: | ||
|[[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]]|4.3.0|'' | + | |[[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 300: | Line 308: | ||
|[[rgi-software|rgi]]|6.0.2|'' | |[[rgi-software|rgi]]|6.0.2|'' | ||
|[[rmblast-software|rmblast]]|2.11.0|'' | |[[rmblast-software|rmblast]]|2.11.0|'' | ||
+ | |[[roary-software|roary]]|3.13.0|'' | ||
|[[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]]|1.3.1|'' | |[[rsem-software|RSEM]]|1.3.1|'' | ||
|[[rseqc-software|rseqc]]|2.6.4|'' | |[[rseqc-software|rseqc]]|2.6.4|'' | ||
- | |[[ruby-software|ruby]]|2.2.3|'' | ||
|[[samtools-software|samtools]]|1.15.1|'' | |[[samtools-software|samtools]]|1.15.1|'' | ||
|[[sailfish-software|sailfish]]|0.9.2|'' | |[[sailfish-software|sailfish]]|0.9.2|'' | ||
Line 321: | Line 329: | ||
|[[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 329: | Line 338: | ||
|[[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|'' | ||
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|[[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 355: | Line 366: | ||
|[[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|'' | + | |[[stringtie2-software|stringtie2]]|2.2.1|'' |
|[[subread-software|subread]]|1.6.2|'' | |[[subread-software|subread]]|1.6.2|'' | ||
|svmlight|V6.02|'' | |svmlight|V6.02|'' | ||
Line 374: | Line 385: | ||
|[[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|'' |
list-of-software.txt · Last modified: 2024/06/19 11:50 by aorth