Cluster Software installed for SBBS

The following software has been installed on Apocrita and is pre-loaded for SBCS users. For non-SBCS users please use the 'module load sbcs' command to put the software in your PATH for the current session.

Use the command "module load" followed by the "Load Command" or "Load Group" you want:

Name	Version	Description	Load Command	Load Groups
454 data anaylysis tools	2.8-1	The GS Data Analysis Software package includes the tools to investigate complex genomic variation in samples including de novo assembly, reference guided alignment and variant calling, and low abundance variant identification and quantification.	Pre-loaded
ABySS	1.3.6	ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads.	abyss/1.3.6	sbcs
AUGUSTUS	2.6.1	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.	augustus/2.6.1	sbcs
bcftools	0.1.17-dev	bcftools - Utilities for the Binary Call Format (BCF) and VCF	bcftools/0.1.17-dev	sbcs
bedtools	2.16.2	bedtools: a flexible suite of utilities for comparing genomic features.	bedtools/2.16.2	sbcs
BioPerl	1.6.901	The Bioperl Project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science	bioperl/1.6.901	sbcs
BLAST+	2.2.26	The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.	blast+/2.2.26	sbcs
Blat	34	Blat quickly maps your sequence to the genome.	blat/34	sbcs
Bowtie	0.12.8 & 1.0.0	Bowtie is an ultrafast, memory-efficient short read aligner.	bowtie/0.12.8 bowtie/1.0.0	sbcs
Bowtie 2	2.0.0-beta6 2.1.0	Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.	bowtie2/2.0.0-beta6 bowtie2/2.1.0	sbcs
BWA	0.6.2 & 0.7.5a	Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.	bwa/0.6.2 or bwa/0.7.5a	sbcs
CEGMA	2.4.010312	Core Eukaryotic Genes Mapping Approach	cegma/2.4.010312	sbcs
ClustalW2	2.1	ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.	clustalw2/2.1	sbcs
cufflinks	2.0.2 & 2.1.1	Transcript assembly, differential expression, and differential regulation for RNA-Seq	cufflinks/2.0.2 cufflnks/2.1.1	sbcs
EMBOSS	6.4.0	The European Molecular Biology Open Software Suite.	emboss/6.4.0	sbcs
exonerate	2.2.0	exonerate is a generic tool for pairwise sequence comparison.	exonerate/2.2.0	sbcs
fasta	36.3.5e	Version 3 of the FASTA packages contains many programs for searching DNA and	fasta/36.3.5e	sbcs
FASTX	0.0.13.2	The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.	fastx/0.0.13.2	sbcs
FSA	1.15.7	FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences.	fsa/1.15.7	sbcs
geneid	1.4.4	geneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure.	geneid/1.4.4	sbcs
GeneWise	02/02/2000	Wise2 is package that is focused on comparing DNA sequences at the level of its conceptual translation, regardless of sequencing error and introns.	genewise/02/02/2000	sbcs
Git	1.7.1	Git is a free and open source distributed version control system	git/1.7.1	sbcs
GNU Parallel	20121122	GNU parallel is a shell tool for executing jobs in parallel using one or more computers. A job can be a single command or a small script that has to be run for each of the lines in the input.	parallel/20121122	sbcs
hmmer	3	Biosequence analysis using profile hidden Markov Models using HMMER.	hmmer/3.0	sbcs
ImageMagick	6.5.4-7	ImageMagick is an open source software suite for displaying, converting, and editing raster image files.	imagemagick/6.5.4-7	sbcs
LaTeX	pdfTeXk 3.14	LaTeX is a document markup language and document preparation system for the TeX typesetting program	latex/pdfTeXk 3.14	sbcs
lftp	4.0.9	LFTP is sophisticated ftp/http client, file transfer program supporting a number of network protocols.	lftp/4.0.9	sbcs
MAFFT	6.903	MAFFT is a multiple sequence alignment program for unix-like operating systems.	mafft/6.903	sbcs
MAKER		MAKER is a portable and easily configurable genome annotation pipeline.	MAKER/2.27	sbcs
MPQC	2.3.1	MPQC is the Massively Parallel Quantum Chemistry Program. It computes properties of atoms and molecules from first principles using the time independent Schrödinger equation.	mpqc/2.3.1	sbcs
MrBayes	3.2.1	MrBayes is a free software program which performs Bayesian inference of phylogeny.	mrbayes/3.2.1	sbcs
MUSCLE	3.8.31	MUSCLE stands for MUltiple Sequence Comparison by Log- Expectation.	muscle/3.8.31	sbcs
MuTect	1.1.4	MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.	mutect/1.1.4	sbcs
Newick Utilities	1.6	The Newick Utilities are a suite of Unix shell tools for processing phylogenetic trees.	newick utilities/1.6	sbcs
NWChem	6.1.1	NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.	nwchem/6.1.1	sbcs
Open Babel	2.3.1	Open Babel is a chemical toolbox designed to speak the many languages of chemical data.	open babel/2.3.1	sbcs
Phrap/Cross_match/Swat	0.990329	phrap is a program for assembling shotgun DNA sequence data. cross_match is a general purpose utility for comparing any two DNA sequence sets using a 'banded' version of swat. swat is a program for searching one or more DNA or protein query sequences, or a query profile, against a sequence database, using an efficient implementation of the Smith-Waterman or Needleman-Wunsch algorithms with linear (affine) gap penalties.	crossmatch	sbcs
PhyloBayes-mpi	1.2f	PhyloBayes (Lartillot et al, 2009) is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction. It is well suited to phylogenomic studies using large multigene alignments.	phylobayes-mpi/1.2f	sbcs
PhyML	3	PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences.	phyml/3	sbcs
PRANK	120626	PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences.	prank/120626	sbcs
R	2.15.0	R is a free software environment for statistical computing and graphics.	Pre-loaded
RAxML	7.2.8-SS3-alpha, 7.4.2-SS3-hybrid, 7.4.2-SS3-pthreads	RAxML (Randomized Axelerated Maximum Likelihood) is a program for Maximum Likelihood-based inference of large phylogenetic trees.	RAxML/7.2.8-alpha RAxML/7.4.2/hybrid RAxML/7.4.2/pthreads	sbcs
RepeatExplorer	10/05/2013	FOR SBCS DOC CLICK HERE RepeatExplorer includes utilities for Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data and tools for the detection of transposable element protein coding domains.	repeatexplorer
RepeatMasker	3.3.0	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.	repeatmasker/3.3.0	sbcs
RMBlast	2.2.23+ 2.2.27	RMBlast supports RepeatMasker searches by adding a few necessary features to the stock NCBI blastn program.	rmblast/2.2.23+ rmblast/2.2.27	sbcs
SAM Tools	0.1.18	SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.	sam tools/0.1.18	sbcs
SNAP	17/05/2012	SNP Annotation and Proxy Search	snap/2012-05-17	sbcs