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| Software | Version | Module | Notes |
|---|---|---|---|
| Augustus | 3.3.2 | bioinformatics/augustus/3.3.2 | installed with conda |
| bbmap | 38.67 | bioinformatics/bbmap/38.67 | installed with conda; environment 'bbmap_38.67' |
| bcftools | 1.9 | bioinformatics/bcftools/1.9 | gcc 7.3.0 |
| Beagle | 3.2 | bioinformatics/beagle/3.2 | gcc 7.3.0 |
| Beast | 1.10.4 2.6.0 | bioinformatics/beast/1.10.4 bioinformatics/beast/2.6.0 | java 1.8.0_45 java 1.8.0_45 |
| bedtools | 2.28.0 | bioinformatics/bedtools/2.28.0 | installed with conda |
| bioperl | 1.7.2 | bioinformatics/bioperl/1.7.2 | installed with conda; environment 'bioperl_1.7.2' |
| biopython | 1.74 | bioinformatics/biopython/1.74 | installed with conda; environment 'biopython_1.74' |
| blasr | 5.3.3 5.0 | bioinformatics/blasr/5.3.3 bioinformatics/blasr/5.0 | installed with conda transferred from Hydra-4 |
| BLAST | 2.6.0 2.9.0 2.8.1 | bioinformatics/blast/2.6.0 bioinformatics/blast/2.9.0 bioinformatics/blast/2.8.1 | gcc 7.3.0 gcc 7.3.0 gcc 7.3.0 |
| blat | 36 | bioinformatics/blat/36 | installed with conda |
| BlobTools | 1.0.1 | bioinformatics/blobtools/1.0.1 | installed with conda; environment 'blobtools_1.0.1' |
| Bowtie2 | 2.3.5 | bioinformatics/bowtie2/2.3.5 | installed with conda |
| BUSCO | 3.0.2 | bioinformatics/busco/3.0.2 | installed with conda; environment 'busco_3.0.2' |
| BWA | 0.7.17 | bioinformatics/bwa/0.7.17 | gcc 7.3.0 |
| cactus | 2019.03.01 | bioinformatics/cactus/2019.03.01 | installed with conda; environment 'cactus_2019.03.01' |
| canu | 1.8 | bioinformatics/canu/1.8 | gcc 7.3.0 |
| Cutadapt | 2.4 | bioinformatics/cutadapt/2.4 | installed with conda |
| FastQC | 0.11.8 | bioinformatics/fastqc/0.11.8 | java 1.8 |
| GATK | 3.8.1.0 4.1.3.0 | bioinformatics/gatk/3.8.1.0 bioinformatics/gatk/4.1.3.0 | java 1.8 java 1.8 |
| Gblocks | 0.91b | bioinformatics/gblocks/0.91b | bioperl added to module |
| GetOrganelle | 1.6.2d | bioinformatics/getorganelle/1.6.2d | installed with conda |
| hmmer | 3.2.1 | bioinformatics/hmmer/3.2.1 | gcc 7.3.0 |
| htslib | 1.9 | bioinformatics/htslib/1.9 | gcc 7.3.0 |
| HybPiper | 1.3 | bioinformatics/hybpiper/1.3 | dependencies installed with conda; environment 'hybpiper' |
| HyPhy | 2.5.1 | bioinformatics/hyphy/2.5.1 | installed with conda; environment 'hyphy_2.5.1' |
| IMPUTE2 | 2.3.2 | bioinformatics/shapeit/2.r837 | installed with conda; environment 'shapeit_2.r837' |
| ipyrad | 0.7.30 0.9.12 | bioinformatics/ipyrad/0.7.30 bioinformatics/ipyrad/0.9 | installed with conda; environment 'ipyrad_0.7.30' installed with conda; environment 'ipyrad_0.9' |
| IQ-TREE | 1.6.12 | bioinformatics/iqtree/1.6.12 | precompiled |
| JBrowse | 1.16.6 | bioinformatics/jbrowse/1.16.6 | installed with conda; environment 'jbrowse_1.16.6' |
| jellyfish | 2.3.0 | bioinformatics/jellyfish/2.3.0 | gcc 7.3.0 |
| julia | 1.2.0 | bioinformatics/julia/1.2.0 | gcc 7.3.0 |
| MAFFT | 7.407 | bioinformatics/mafft/7.407 | installed with conda |
| MaSuRCA | 3.3.3 | bioinformatics/masurca/3.3.3 | gcc 7.3.0 |
| MrBayes | 3.2.7a | bioinformatics/mrbayes/3.2.7a | gcc 7.3.0, mvapich 7.3 |
| migrate | 3.7.2 4.4.4 3.6.11 | bioinformatics/migrate/3.7.2 bioinformatics/migrate/4.4.4 bioinformatics/migrate/3.6.11 | gcc 7.3.0, mpich 7.3 gcc 7.3.0, mpich 7.3 gcc 4.9.2 (no MPI version) |
| Orthofinder | 2.2.7 | bioinformatics/orthofinder/2.2.7 | installed with conda; environment 'orthofinder_2.2.7' |
| OrthoMCL | 2.0.9 | bioinformatics/orthomcl/2.0.9 | installed with conda; environment 'orthomcl_2.0.9' |
| PAML | 4.9 | bioinformatics/paml/4.9 | installed with conda; environment 'paml_4.9' |
| Partitionfinder | 2.1.1 | bioinformatics/partitionfinder/2.1.1 | added python 2.7 to module |
| Phylobayes | 4.1c | bioinformatics/phylobayes/4.1c | installed with conda; environment 'phylobayes_4.1c' |
| Phyluce | 1.6.7 1.5_tg | bioinformatics/phyluce/1.6.7 bioinformatics/phyluce/1.5_tg | installed with conda; environment 'phyluce_1.6.7' transferred from Hydra-4 |
| Picard-tools | 2.20.6 | bioinformatics/picard-tools/2.20.6 | java 1.8 |
| Pilon | 1.23 | bioinformatics/pilon/1.23 | java 1.8 |
| Proteinortho | 6.0.6 | bioinformatics/proteinortho/6.0.6 | installed with conda; environment 'proteinortho_6.0.6' |
| PSMC | 0.6.5 | bioinformatics/psmc/0.6.5 | gcc 7.3.0 |
| Python | 2.7 2.7_mpi 3.6 | bioinformatics/python/2.7 bioinformatics/python/2.7_mpi bioinformatics/python/3.6 | installed with conda; environment 'py2' installed with conda; environment 'py2_mpi' installed with conda; environment 'py3' |
| QIIME2 | 2019.7 | bioinformatics/qiime2/2019.7 | installed with conda; environment 'qiime2-2019.7' |
| R | 3.6.1 | bioinformatics/R/3.6.1 | gcc 7.3.0, java 1.8 |
| RAxML | 8.2.12 8.2.12-mpi ng-0.9.0 | bioinformatics/raxml/8.2.12 bioinformatics/raxml/8.2.12-mpi bioinformatics/raxml/ng-0.9.0 | gcc 7.3.0 mpich 7.3 precompiled |
| RepeatMasker | 4.0.9 | bioinformatics/repeatmasker/4.0.9 | |
| revbayes | 1.0.11 | bioinformatics/revbayes/1.0.11 | gcc 4.9.2, cmake 3.31 |
| Ruby | 2.6.3 | bioinformatics/ruby/2.6.3 | gcc 7.3.0 |
| salmon | 0.14.1 | bioinformatics/salmon/0.14.1 | installed with conda; environment 'salmon_0.14.1' |
SHAPEIT | 2.r837 | bioinformatics/shapeit/2.r837 | installed with conda; environment 'shapeit_2.r837' |
| smc++ | 1.15.2 | bioinformatics/smc++/1.15.2 | installed with conda; environment 'smc++_1.15.2' |
| Stacks | 1.48 2.4.1 | bioinformatics/stacks/1.48 bioinformatics/stacks/2.4.1 | gcc 7.3.0 gcc 7.3.0 |
| Structure | 2.3.4 | bioinformatics/structure/2.3.4 | |
| Supernova | 2.1.1 | bioinformatics/supernova/2.1.1 | precompiled |
| Transdecoder | 5.5.0 | bioinformatics/transdecoder/5.5.0 | bioperl, BLAST added to module |
| TrimGalore! | 0.6.4 | bioinformatics/trim_galore/0.6.4 | FastQC, Cutadapt added to module |
| Trimmomatic | 0.39 | bioinformatics/trimmomatic/0.39 | java 1.8 |
| Trinity | 2.8.5 r2013_2_25 | bioinformatics/trinity/2.8.5 bioinformatics/trinity/r2013_2_25 | installed with conda; environment 'trinity_2.8.5' transferred from Hydra-4 |
| Trinotate | 3.2.0 | bioinformatics/trinotate/3.2.0 | bioperl added to module |
| vcflib | 1.0.0-rc3 | bioinformatics/vcflib/1.0.0-rc3 | gcc 7.3.0 |
| vcftools | 0.1.16 | bioinformatics/vcftools/0.1.16 | gcc 7.3.0 |
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