list-of-software
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list-of-software [2022/06/27 13:15] – aorth | list-of-software [2023/02/20 12:19] – aorth | ||
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|[[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-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|'' | ||
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|[[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|'' | ||
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|[[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 110: | ||
|[[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]]|1.8.9|'' | + | |[[funannotate-software|funannotate]]|1.8.11|See software page| | |
|[[gassflow-software|GassFlow ]]|1.0|'' | |[[gassflow-software|GassFlow ]]|1.0|'' | ||
- | |[[gatk-software|gatk]]|4.2.2.0|'' | + | |[[gatk-software|gatk]]|4.3.0.0|'' |
|[[gapfiller-software|gapfiller]]|1.10|'' | |[[gapfiller-software|gapfiller]]|1.10|'' | ||
|[[geneid-software|geneid]]|1.4.4|'' | |[[geneid-software|geneid]]|1.4.4|'' | ||
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|[[gtdbtk-software|gtdbtk]]|1.1.1|'' | |[[gtdbtk-software|gtdbtk]]|1.1.1|'' | ||
|[[guidance-software|guidance]]|2.02|'' | |[[guidance-software|guidance]]|2.02|'' | ||
- | |[[guppy-software|guppy]]|6.0.1|'' | + | |[[guppy-software|guppy]]|6.2.1|'' |
|[[halcyon-software|halcyon]]|0.1.1|'' | |[[halcyon-software|halcyon]]|0.1.1|'' | ||
|[[hapflk-software|hapflk]]|1.4|'' | |[[hapflk-software|hapflk]]|1.4|'' | ||
Line 164: | Line 166: | ||
|[[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|'' | ||
|[[kmer-ssr-software|kmer-ssr]]|git-4043c0e7|'' | |[[kmer-ssr-software|kmer-ssr]]|git-4043c0e7|'' | ||
- | |[[kraken-software|kraken]]|2.0.8-beta|'' | + | |[[kraken-software|kraken]]|2.1.2|'' |
|[[krona-software|krona]]|2.8.1|'' | |[[krona-software|krona]]|2.8.1|'' | ||
|lamp|2.5|'' | |lamp|2.5|'' | ||
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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|'' | ||
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|[[migmap-software|migmap]]|1.0.2|'' | |[[migmap-software|migmap]]|1.0.2|'' | ||
|[[miniasm-software|miniasm]]|0.3|'' | |[[miniasm-software|miniasm]]|0.3|'' | ||
+ | |[[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]]|2.22|'' | ||
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|[[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|'' | ||
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|[[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|'' | ||
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|[[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]]|3.8.11|'' | + | |[[python-software|python]]|3.9.14|'' |
|qdd|3_beta|'' | |qdd|3_beta|'' | ||
|[[qiime-software|qiime]]|1.9.1|'' | |[[qiime-software|qiime]]|1.9.1|'' | ||
Line 280: | Line 285: | ||
|[[r-software|R]]|4.2.0|'' | |[[r-software|R]]|4.2.0|'' | ||
|[[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|'' | ||
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|[[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|'' | ||
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|[[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|'' | ||
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|[[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 339: | Line 347: | ||
|[[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|'' | ||
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|[[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|'' |
list-of-software.txt · Last modified: 2024/06/19 11:50 by aorth