list-of-software
Differences
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list-of-software [2022/09/20 07:32] – aorth | list-of-software [2023/05/22 06:11] – 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 43: | Line 46: | ||
|[[blast-software|blast]]|2.12.0+|'' | |[[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|'' |
|[[bmtagger-software|bmtagger]]|0.3.102.4|'' | |[[bmtagger-software|bmtagger]]|0.3.102.4|'' | ||
- | |[[bowtie-software|bowtie1 ]]|1.2.3|'' | + | |[[bowtie-software|bowtie1]]|1.2.3|'' |
- | |[[bowtie2-software|bowtie2 ]]|2.3.4.1|'' | + | |[[bowtie2-software|bowtie2]]|2.5.0|'' |
|[[brig-software|brig]]|0.95|'' | |[[brig-software|brig]]|0.95|'' | ||
|[[busco-software|BUSCO ]]|5.2.2|'' | |[[busco-software|BUSCO ]]|5.2.2|'' | ||
Line 82: | Line 85: | ||
|[[eagle-software|eagle]]|2.4.1|'' | |[[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|'' | |[[emblmygff3-software|emblmygff3]]|2.1|'' | ||
Line 108: | Line 112: | ||
|[[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]]|4.2.2.0|'' | + | |[[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 144: | Line 148: | ||
|[[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|'' | ||
Line 164: | Line 169: | ||
|[[karect-software|karect]]|1.0|'' | |[[karect-software|karect]]|1.0|'' | ||
|[[kat-software|kat]]|2.3.4|'' | |[[kat-software|kat]]|2.3.4|'' | ||
- | |[[kma-software|kma]]|1.4.0|'' | + | |[[kma-software|kma]]|1.4.11|'' |
|[[kmc-software|kmc]]|3.1.1|'' | |[[kmc-software|kmc]]|3.1.1|'' | ||
|[[kmergenie-software|kmergenie]]|1.7038|'' | |[[kmergenie-software|kmergenie]]|1.7038|'' | ||
Line 175: | Line 180: | ||
|[[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 204: | Line 210: | ||
|[[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 220: | Line 226: | ||
|[[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]]|22.10 (22.10.8)|'' |
|[[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 235: | Line 241: | ||
|[[oases-software|oases]]|0.2.08|'' | |[[oases-software|oases]]|0.2.08|'' | ||
|[[ocaml-software# | |[[ocaml-software# | ||
+ | |[[oligoarrayaux-software|oligoarrayaux]]|3.8.1|'' | ||
|[[opam-software# | |[[opam-software# | ||
|orthomcl|2.0.3|'' | |orthomcl|2.0.3|'' | ||
Line 253: | Line 260: | ||
|[[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]]|2.26.1|'' | + | |[[picard-software|picard]]|2.27.5|'' |
|[[picrust-software# | |[[picrust-software# | ||
|[[pilon-software|pilon]]|1.23|'' | |[[pilon-software|pilon]]|1.23|'' | ||
Line 261: | Line 268: | ||
|[[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|'' | ||
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|[[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]]|4.3.0|'' |
|[[racon-software|racon]]|1.3.1|'' | |[[racon-software|racon]]|1.3.1|'' | ||
- | |[[rmblast-software|rmblast]]|2.11.0|'' | ||
|[[rapsearch-software|rapsearch]]|2.22|'' | |[[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|'' | ||
|[[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|'' | ||
|[[recon-software|recon]]|1.08|'' | |[[recon-software|recon]]|1.08|'' | ||
Line 291: | Line 298: | ||
|[[repeatmodeler-software|repeatmodeler]]|2.0.1|'' | |[[repeatmodeler-software|repeatmodeler]]|2.0.1|'' | ||
|[[repseqio-software|repseqio]]|1.3.3|'' | |[[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|'' | ||
Line 311: | Line 320: | ||
|[[seqwish-software|seqwish]]|0.6|'' | |[[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|'' | |[[shasta-software|shasta]]|0.4.0|'' | ||
|[[sickle-software|sickle]]|1.33|'' | |[[sickle-software|sickle]]|1.33|'' | ||
Line 329: | Line 339: | ||
|[[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]]|3.15 (3.15.4)|'' | + | |[[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|'' | ||
Line 340: | Line 350: | ||
|[[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]]|2.7.10a|'' | |[[star-software|star]]|2.7.10a|'' | ||
Line 354: | Line 364: | ||
|[[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|'' | ||
Line 371: | Line 382: | ||
|[[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