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list-of-software [2018/07/03 12:01]
aorth
list-of-software [2018/11/16 17:48] (current)
aorth
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 |bayescan|2.1|''​module load bayescan/​2.1''​| | |bayescan|2.1|''​module load bayescan/​2.1''​| |
 |[[bcftools-software|bcftools]]|1.8|''​module load bcftools/​1.8''​| | |[[bcftools-software|bcftools]]|1.8|''​module load bcftools/​1.8''​| |
-|[[beagle-software|beagle]]|2.1.2|''​module load beagle/2.1.2''​| | +|[[beagle-software|beagle]]|3.0.2|''​module load beagle/3.0.2''​| | 
-|[[beast-software|beast]]|1.8.3|''​module load beast/1.8.3''​| |+|[[beast-software|beast]]|1.10.2|''​module load beast/1.10.2''​| |
 |[[bedops-software|bedops]]|2.4.29|''​module load bedops/​2.4.29''​| | |[[bedops-software|bedops]]|2.4.29|''​module load bedops/​2.4.29''​| |
 |[[bedtools-software|bedtools]]|2.25.0|''​module load bedtools/​2.25.0''​| | |[[bedtools-software|bedtools]]|2.25.0|''​module load bedtools/​2.25.0''​| |
Line 43: Line 43:
 |[[cafe-software|cafe]]|4.1|''​module load cafe/​4.1''​| | |[[cafe-software|cafe]]|4.1|''​module load cafe/​4.1''​| |
 |cangs|1.1|''​module load cangs/​1.1''​| | |cangs|1.1|''​module load cangs/​1.1''​| |
-|[[canu-software|canu]]|1.6|''​module load canu/1.6''​| |+|[[canu-software|canu]]|1.8|''​module load canu/1.8''​| |
 |cap3|latest|''​module load cap3/​latest''​| | |cap3|latest|''​module load cap3/​latest''​| |
-|[[cd-hit-software|cd-hit]]|4.6.6|''​module load cd-hit/4.6.6''​| |+|[[cd-hit-software|cd-hit]]|4.6.8|''​module load cd-hit/4.6.8''​| |
 |[[cegma-software|cegma]]|v2.5|''​module load cegma/​v2.5''​| | |[[cegma-software|cegma]]|v2.5|''​module load cegma/​v2.5''​| |
 |celera-wgs|6.1|''​module load celera-wgs/​6.1''​| | |celera-wgs|6.1|''​module load celera-wgs/​6.1''​| |
Line 61: Line 61:
 |cufflinks|2.2.1|''​module load cufflinks/​2.2.1''​| | |cufflinks|2.2.1|''​module load cufflinks/​2.2.1''​| |
 |[[cutadapt-software|cutadapt]]|v1.8.1|''​module load cutadapt/​v1.8.1''​| | |[[cutadapt-software|cutadapt]]|v1.8.1|''​module load cutadapt/​v1.8.1''​| |
 +|[[dextractor-software|dextractor]]|git-a7f50c52|''​module load dextractor/​git-a7f50c52''​| |
 |dendroscope|2.7.4|''​module load dendroscope/​2.7.4''​| | |dendroscope|2.7.4|''​module load dendroscope/​2.7.4''​| |
 |[[diamond-software|diamond]]|0.9.9|''​module load diamond/​0.9.9''​| | |[[diamond-software|diamond]]|0.9.9|''​module load diamond/​0.9.9''​| |
Line 72: Line 73:
 |[[express-software|express]]|1.5.1|''​module load express/​1.5.1''​| | |[[express-software|express]]|1.5.1|''​module load express/​1.5.1''​| |
 |[[fastPHASE-software|fastPHASE]]|1.4.8|''​module load fastPHASE/​1.4.8''​| | |[[fastPHASE-software|fastPHASE]]|1.4.8|''​module load fastPHASE/​1.4.8''​| |
-|[[fastqc-software|fastqc]]|0.11.5|''​module load fastqc/​0.11.5''​| |+|[[fastqc-software|fastqc]]|0.11.7|''​module load fastqc/​0.11.7''​| |
 |[[faststructure-software|fastSTRUCTURE]]|1.0|''​module load fastSTRUCTURE/​1.0''​| | |[[faststructure-software|fastSTRUCTURE]]|1.0|''​module load fastSTRUCTURE/​1.0''​| |
 |[[fastx-toolkit-software|fastx_toolkit]]|0.0.13|''​module load fastx_toolkit/​0.0.13''​| | |[[fastx-toolkit-software|fastx_toolkit]]|0.0.13|''​module load fastx_toolkit/​0.0.13''​| |
Line 85: Line 86:
 |[[freebayes-software|FreeBayes ]]|1.0.2|''​module load freebayes/​1.0.2''​| | |[[freebayes-software|FreeBayes ]]|1.0.2|''​module load freebayes/​1.0.2''​| |
 |[[gassflow-software|GassFlow ]]|1.0|''​module load gassflow/​1.0''​| | |[[gassflow-software|GassFlow ]]|1.0|''​module load gassflow/​1.0''​| |
-|[[gatk-software|GATK ]]|3.7.0|''​module load gatk/3.7.0''​| |+|[[gatk-software|GATK ]]|4.0.10.1|''​module load gatk/4.0.10.1''​| |
 |[[gapfiller-software|gapfiller]]|1.10|''​module load gapfiller/​1.10''​| | |[[gapfiller-software|gapfiller]]|1.10|''​module load gapfiller/​1.10''​| |
 |[[geneid-software|geneid]]|1.4.4|''​module load geneid/​1.4.4''​| | |[[geneid-software|geneid]]|1.4.4|''​module load geneid/​1.4.4''​| |
Line 93: Line 94:
 |glu|1.0b3-prerelease4|''​module load glu/​1.0b3-prerelease4''​| | |glu|1.0b3-prerelease4|''​module load glu/​1.0b3-prerelease4''​| |
 |[[gmap-software|gmap]]|2015-12-31|''​module load gmap/​2015-12-31''​| | |[[gmap-software|gmap]]|2015-12-31|''​module load gmap/​2015-12-31''​| |
 +|[[graphmap-software|graphmap]]|0.5.2|''​module load graphmap/​0.5.2''​| |
 |[[grom-rd-software|grom-rd]]|1.0|''​module load grom-rd/​1.0''​| | |[[grom-rd-software|grom-rd]]|1.0|''​module load grom-rd/​1.0''​| |
 +|[[gromacs-software|gromacs]]|2018.2|''​module load gromacs/​2018.2''​| |
 |[[groovy-software|groovy]]|2.4.9|''​module load groovy/​2.4.9''​| | |[[groovy-software|groovy]]|2.4.9|''​module load groovy/​2.4.9''​| |
 |[[gsea-software|GSEA]]|2.2.3|''​module load gsea/​2.2.3''​| | |[[gsea-software|GSEA]]|2.2.3|''​module load gsea/​2.2.3''​| |
Line 102: Line 105:
 |[[hmmer-software|hmmer]]|3.1b2|''​module load hmmer/​3.1b2''​| | |[[hmmer-software|hmmer]]|3.1b2|''​module load hmmer/​3.1b2''​| |
 |[[hpg-variant-software|hpg-variant]]|1.0|''​module load hpg-variant/​1.0''​| | |[[hpg-variant-software|hpg-variant]]|1.0|''​module load hpg-variant/​1.0''​| |
-|[[hisat2-software|hisat2]]|2.0.5|''​module load hisat2/2.0.5''​| |+|[[hisat2-software|hisat2]]|2.1.0|''​module load hisat2/2.1.0''​| |
 |[[htseq-software|htseq]]|0.6.1|''​module load htseq/​0.6.1''​| | |[[htseq-software|htseq]]|0.6.1|''​module load htseq/​0.6.1''​| |
 |[[htslib-software|htslib]]|1.8|''​module load htslib/​1.8''​| | |[[htslib-software|htslib]]|1.8|''​module load htslib/​1.8''​| |
Line 129: Line 132:
 |[[mafft-software|mafft]]|7.313|''​module load mafft/​7.313''​| | |[[mafft-software|mafft]]|7.313|''​module load mafft/​7.313''​| |
 |[[mapsplice-software|mapsplice]]|2.2.0|''​module load mapsplice/​2.2.0''​| | |[[mapsplice-software|mapsplice]]|2.2.0|''​module load mapsplice/​2.2.0''​| |
 +|[[marginalign-software|marginalign]]|git-2369dafd|''​module load marginalign/​git-2369dafd''​| |
 |[[mash-software|mash]]|2.0|''​module load mash/​2.0''​| | |[[mash-software|mash]]|2.0|''​module load mash/​2.0''​| |
 +|[[masurca-software|masurca]]|3.2.8|''​module load masurca/​3.2.8''​| |
 |mauve|2.3.1|''​module load mauve/​2.3.1''​| | |mauve|2.3.1|''​module load mauve/​2.3.1''​| |
-|[[masurca-software|masurca]]|2.3.2|''​module load masurca/​2.3.2''​| | 
 |maximus|0.2|''​module load maximus/​0.2''​| | |maximus|0.2|''​module load maximus/​0.2''​| |
-|[[megahit-software|megahit]]|git-02102e1b|''​module load megahit/git-02102e1b''​| |+|[[mcl-software|mcl]]|14-137|''​module load mcl/​14-137''​| | 
 +|[[mecat-software|MECAT]]|git-d04bfa84|''​module load MECAT/git-d04bfa84''​| | 
 +|[[megahit-software|megahit]]|1.1.4|''​module load megahit/​1.1.4''​| |
 |megan|4.70.4|''​module load megan/​4.70.4''​| | |megan|4.70.4|''​module load megan/​4.70.4''​| |
 |[[metabat-software|metabat]]|2.12.1|''​module load metabat/​2.12.1''​| | |[[metabat-software|metabat]]|2.12.1|''​module load metabat/​2.12.1''​| |
Line 139: Line 145:
 |[[migec-software|migec]]|1.2.4a|''​module load migec/​1.2.4a''​| | |[[migec-software|migec]]|1.2.4a|''​module load migec/​1.2.4a''​| |
 |[[migmap-software|migmap]]|1.0.2|''​module load migmap/​1.0.2''​| | |[[migmap-software|migmap]]|1.0.2|''​module load migmap/​1.0.2''​| |
 +|[[miniasm-software|miniasm]]|0.3|''​module load miniasm/​0.3''​| |
 +|[[minimap2-software|minimap2]]|2.13|''​module load minimap2/​2.13''​| |
 |[[minpath-software|MinPath]]|1.0.2|''​module load MinPath/​1.2''​| | |[[minpath-software|MinPath]]|1.0.2|''​module load MinPath/​1.2''​| |
 |[[mira-software#​v4.0.2|mira ]]|4.0.2|''​module load mira/​4.0.2''​| | |[[mira-software#​v4.0.2|mira ]]|4.0.2|''​module load mira/​4.0.2''​| |
Line 165: Line 173:
 |[[paml-software|paml]]|4.9a|''​module load paml/​4.9a''​| | |[[paml-software|paml]]|4.9a|''​module load paml/​4.9a''​| |
 |[[pandaseq-software|pandaseq]]|2.8.1|''​module load pandaseq/​2.8.1''​| ​ | |[[pandaseq-software|pandaseq]]|2.8.1|''​module load pandaseq/​2.8.1''​| ​ |
 +|[[pasta-software|pasta]]|d939adb2|''​module load pasta/​d939adb2''​| ​ |
 |[[pear-software|pear]]|git-2c309dc|''​module load pear/​git-2c309dc''​| | |[[pear-software|pear]]|git-2c309dc|''​module load pear/​git-2c309dc''​| |
 |[[pbsuite-software|pbsuite]]|15.8.24|''​module load pbsuite/​15.8.24''​| | |[[pbsuite-software|pbsuite]]|15.8.24|''​module load pbsuite/​15.8.24''​| |
Line 172: Line 181:
 |phred|0.990722.f|''​module load phred/​0.990722.f''​| | |phred|0.990722.f|''​module load phred/​0.990722.f''​| |
 |[[phylip-software|phylip]]|3.696|''​module load phylip/​3.696''​| | |[[phylip-software|phylip]]|3.696|''​module load phylip/​3.696''​| |
-|[[phyml-software|phyml]]|20120412|''​module load phyml/20120412''​| |+|[[phyml-software|phyml]]|3.3.20180621|''​module load phyml/3.3.20180621''​| |
 |[[picard-software|picard]]|2.17.0|''​module load picard/​2.17.0''​| | |[[picard-software|picard]]|2.17.0|''​module load picard/​2.17.0''​| |
 |[[picrust-software#​v1.0.0|picrust]]|1.0.0|''​module load picrust/​1.0.0''​| | |[[picrust-software#​v1.0.0|picrust]]|1.0.0|''​module load picrust/​1.0.0''​| |
Line 183: Line 192:
 |[[prokka-software|prokka]]|1.11|''​module load prokka/​1.11''​| | |[[prokka-software|prokka]]|1.11|''​module load prokka/​1.11''​| |
 |[[provean-software|provean]]|1.1.5|''​module load provean/​1.1.5''​| | |[[provean-software|provean]]|1.1.5|''​module load provean/​1.1.5''​| |
-|[[python-software|python]]|3.6.2|''​module load python/3.6.2''​| |+|[[python-software|python]]|3.7.1|''​module load python/3.7''​| |
 |qdd|3_beta|''​module load qdd/​3_beta''​| | |qdd|3_beta|''​module load qdd/​3_beta''​| |
 |[[qiime-software|qiime]]|1.9.1|''​module load qiime/​1.9.1''​| | |[[qiime-software|qiime]]|1.9.1|''​module load qiime/​1.9.1''​| |
-|[[qiime2-software|qiime2]]|2018.4|''​module load qiime2/​2018.4''​| |+|[[qiime2-software|qiime2]]|2018.6|''​module load qiime2/​2018.6''​| |
 |[[quast-software|quast]]|4.5|''​module load quast/​4.5''​| | |[[quast-software|quast]]|4.5|''​module load quast/​4.5''​| |
 |[[quorum-software|Quorum]]|1.1.1|''​module load quorum/​1.1.1''​| | |[[quorum-software|Quorum]]|1.1.1|''​module load quorum/​1.1.1''​| |
Line 194: Line 203:
 |rapsearch|2.10|''​module load rapsearch/​2.10''​| | |rapsearch|2.10|''​module load rapsearch/​2.10''​| |
 |[[ratt-software|RATT]]|r18|''​module load ratt/​r18''​| | |[[ratt-software|RATT]]|r18|''​module load ratt/​r18''​| |
-|[[raxml-software|RAxML]]|8.2.0|''​module load RAxML/8.2.0''​| |+|[[raxml-software|RAxML]]|8.2.12|''​module load RAxML/8.2.12''​| |
 |[[ray-software|ray]]|2.3.1|''​module load ray/​2.3.1''​| | |[[ray-software|ray]]|2.3.1|''​module load ray/​2.3.1''​| |
 |[[rdp-classifier-software|RDP Classifier]]|2.11|''​module load rdp-classifier/​2.11''​| | |[[rdp-classifier-software|RDP Classifier]]|2.11|''​module load rdp-classifier/​2.11''​| |
Line 237: Line 246:
 |[[stacks-software|stacks]]|1.24|''​module load stacks/​1.24''​| | |[[stacks-software|stacks]]|1.24|''​module load stacks/​1.24''​| |
 |staden|2.0.0b8|''​module load staden/​2.0.0b8''​| | |staden|2.0.0b8|''​module load staden/​2.0.0b8''​| |
-|[[star-software|star]]|2.5.2b|''​module load star/2.5.2b''​| |+|[[star-software|star]]|2.5.3a|''​module load star/2.5.3a''​| |
 |[[structure-software|structure]]|2.3.4|''​module load structure/​2.3.4''​| ​ | |[[structure-software|structure]]|2.3.4|''​module load structure/​2.3.4''​| ​ |
 |[[stringtie-software|stringtie]]|1.3.4d|''​module load stringtie/​1.3.4d''​| | |[[stringtie-software|stringtie]]|1.3.4d|''​module load stringtie/​1.3.4d''​| |
 +|[[subread-software|subread]]|1.6.2|''​module load subread/​1.6.2''​| |
 |svmlight|V6.02|''​module load svmlight/​V6.02''​| | |svmlight|V6.02|''​module load svmlight/​V6.02''​| |
 |tabix|git-76b4bbdf|''​module load tabix/​git-76b4bbdf''​| | |tabix|git-76b4bbdf|''​module load tabix/​git-76b4bbdf''​| |
list-of-software.1530608462.txt.gz · Last modified: 2018/07/03 12:01 by aorth