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Available Software
Before any software can be used, the corresponding module has to be loaded. This is done by typing module load software_name. You can use module avail or module whatis to list the names of the available software modules. To list the modules currently loaded, use module list
In many cases you will need to submit your jobs to GridEngine. This is the case when the runtime exceeds 30 minutes or the memory requirement exceeds 2GB.
Please edit the software pages and add notes if you find the information incomplete, or if you want to share any specifics on how the software is used.
Alignment
- Software/Mafft - Multiple sequence alignment program (Version 7.450)
- Software/Mauve - Multiple alignment of genomes
Classification
- Software/GraftM - Pipeline to identify and classify marker gene reads from metagenomic datasets (Version 0.13.1)
Graphs
- Software/Krona - Set of scripts to create Krona charts (Version May 2019)
Phylogeny
- Software/IQ-TREE - Efficient software for phylogenomic inference (Version 1.6.12)
- Software/FastTreeMP - Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. (Version 2.1.11)
- Software/OrthoFinder - Infers orthogroups, gene trees of orthogroups and species trees from proteomes. (Version 2.3.8)
- Software/Pplacer - Phylogenetic placement (Version 1.1.19)
- Software/gappa - Placements of short environmental sequences on a reference phylogenetic tree (Version 0.6.1)
Sequence analysis
- Software/Diamond - Sequence aligner for protein and translated DNA searches (Version 0.9.26)
- Software/Fxtract - Extract sequences from a fastx file given a subsequence or identifier (Version 2.3)
- Software/HMMER - Biosequence analysis using profile hidden Markov models (Version 3.2.1)
- Software/OrfM - A simple and not slow open reading frame (ORF) caller (Version 0.7.1)
- Software/RECON - Software for repeat finding in genomic sequences (please check Software/RepeatModeler)
- Software/RepeatScout - Software for repeat find in genomic sequences (please check Software/RepeatModeler)
- Software/RepeatMasker - The de facto standard software for repeat masking of genomic sequences
- Software/RepeatModeler - The de-novo repeat family identification and modeling package.
- Software/TRF - Software for finding tandem repeats in genomic sequences
- Software/mfqe - FASTA/FASTQ extractor for multiple sets of read names (Version 0.5.0)
- Software/Infernal - Inference of RNA alignments
- Software/BCFtools - Analysis and handling of VCF/BCF (Variant Call Format) files
Sequence and Genome Annotation tools
- Software/Augustus - Gene pretiction
- Software/InterProScan - Functional annotation of gene sequences (5.48 with database release 83.0)
- Software/tRNAScan-SE - Annotate tRNAs in DNA sequence (version 2.0.7)
Assembly tools -- genome and transcriptome assembly
- Software/ABySS - ABySS short read assembler
- Software/MEGAHIT - Megahit metagenome assembler
- Software/MetaBat2 - Metabat 2 metagenome assembly binning algorithm
- Software/SOAPdenovo2 - SOAPdenovo short read assembler
- Software/SPAdes - SPAdes short read de novo assembler
- Software/Velvet - Velvet short read assembler
Statistics
- Software/R - The R language for statistical computing (Versions: 3.6.0)
Perl
- Software/Perl - The Perl programming language (Version 5.30.0)
Python
Sequencing
Compilers, Libraries, and Other Misc software
Legacy
The following software and modules used to be available before the grid upgrade. They have not been tested on the new grid, but may work without any issues. If you need to use them. Please try out. To load them, first load the module load the module "legacy", and then the appropriate module. If the software fails, please ask create an issue here in Trac and ask for the software or drop a mail to Les.
AEGeAn/0.9.3 emboss/6.6.0 openmpi/2.0.3 (D) AEGeAn/0.9.4 (D) exabayes/1.5 openpyxl/2.2.2 PBSuite/14.6.24 exonerate/2.2.0 orthofinder/1.1.8 R/2.12.0 fastme/2.1.5 orthomcl/2.0.8 R/2.15.1 fastqc/0.10.1 p/mykopat-gbrowse R/3.0.2 (D) fastqc/0.11.5 (D) paml/4.7 R/3.2.0 faststructure/1.0 parallelfork/1.1 R/3.4.1 fastx_toolkit/0.0.13.2 pbh5tools/0.8.0 abyss/1.3.4 filespeclink/filespeclink pear/0.9.10 abyss/1.3.5_kmer128 flexbar/3.0.3 perl/5.16.1 abyss/1.3.5 frc_align/20130408 perl/5.16.2 (D) abyss/1.3.6_kmer128 freebayes/0.9.6 phylip/3.695 abyss/1.3.6 (D) freebayes/0.9.21 picardtools/1.107 amos/3.1.0 freebayes/1.0.0-19-gefe685d (D) picardtools/2.10.0 (D) antismash/2.0.2 gatk/2.8-1 pysam/0.7.4 antismash/3.0.5.1 (D) gatk/3.7.0 python/2.7.3 augustus/2.6.1 gatk/4.0.5.1 (D) python3/3.3.2 augustus/2.7 gcc/7.1.0 python3/3.3.3 augustus/3.0.3 (D) geneid/1.4.4_110113 pyvcf-py3/0.6.7 bamm/2.5.0 genometools/1.5.2 pyvcf/0.6.3 bamtools/2.2.3 glimmer/3.0.2 qiime/1.7.0 bcftools/1.2 glimmerhmm/3.0.2 qiime/1.8.0 beast/1.8.4 gmake/3.82 qiime/1.9.1 (D) bedtools/2.16.2 gmes/2.3e quast/2.3 bioperl/00-2.1.8 grinder/0.5.4 repseek/091209 bioperl/1.6.901-p5162 (D) gsnap/2013-11-27 rocker/1.1.12 biopython-py3/1.63 hdf5/1.8.13 salmon/0.9.1 biopython-py3/1.65 hisat2/2.0.4 samtools/0.1.18 biopython/1.60 hisat2/2.1.0 (D) samtools/1.2 biopython/1.64 hmmer2/2.3.2 samtools/1.8 (D) biopython/1.66 (D) hmmer3/3.0 scipy-py3/0.13.1 blasr/2014.07.09 htslib/1.8 scipy/0.11.0rc2 blast2go iprscan/4.8_db39 seqtk/seqtk blat/35 iqtree/1.5.5 sga/0.10.1 bowtie/0.12.9 jre/1.6.0_39 sina/1.2.11 bowtie2/2.0.0-beta7 jre/1.7.0_11 snap/2012-05-17 bowtie2/2.0.2 jre/1.7.0_51 soapdenovo/1.05 bowtie2/2.1.0 jre/1.8.0_60 (D) solexaqa/3.1.7 bowtie2/2.2.3 kallisto/0.45 spades/3.6.0 bowtie2/2.2.4 legacy-blast/2.2.26 structure/2.3.4 bowtie2/2.3.2 (D) libfuse3/3.2.0 structure/2.3.4.1 (D) bwa/0.5.10 mafft/6.94 tassel/5.0 bwa/0.6.2 matplotlib-py3/1.3.1 tophat/2.0.3.1 bwa/0.7.4 (D) matplotlib/1.2.0rc1 (D) tophat/2.0.6 bzip2c/1.0.6 mavid/2.0.4 tophat/2.0.9 cafe/2.2 mcl/12.068 tophat/2.0.11 cafe/3.1 (D) meme/4.10.0 tophat/2.0.13 (D) cdhit/4.6.1 mercator/2013.01.11 trac/1.0.1
