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Software - Bioinformatics

BioPerl

BioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl. It is prepackaged as part of the cluster software, Rocks, and is available within the cluster. The cluster has two versions of perl, the system version as part of the base operating system and the Rocks version upon which BioPerl is built. The listed command is the Rocks perl that must be used. Below is an example of BioPerl script:

Software Homepage: http://www.bioperl.org/wiki/Main_Page
Available on: Cheetah Cluster
Command: /opt/rocks/bin/perl
Location: /opt/rocks/lib/perl5/site_perl/5.10.1/Bio/


Biopython

Biopython is a set of python modules for bioinformatics computation. The cluster has different versions of python, the system version as part of the base operating system and the Rocks version upon which Biopython is built. To use the Rocks Python, first use: $ module load biopython. Then you can launch python and load Biopython. Below is an example converting GenBank to FASTA:

Software Homepage: http://biopython.org/wiki/Main_Page
Available on: Cheetah Cluster
Command: module load biopython


ClustalW

ClustalW is a multiple sequence alignment program. See the Rocks Cluster Bio User Guide for simple instructions.

Software Homepage: http://www.ebi.ac.uk/Tools/msa/clustalw2/
Available on: Cheetah Cluster
Command: clustalw2
Location: /opt/bio/clustalw


COPASI

COPASI is a software application for simulation and analysis of biochemical networks and their dynamics. It is a stand-alone program that supports models in the SBML standard and can simulate their behavior using ODEs or Gillespie's stochastic simulation algorithm; arbitrary discrete events can be included in such simulations. See the User Manual for instructions.

Software Homepage: http://www.copasi.org
Available on: Cheetah Cluster
Command: CopasiSE, CopasiUI


EMBOSS

EMBOSS (European Molecular Biology Open Software Suite) is a set of tools that are used for sequence analysis.

Software Homepage: http://emboss.sourceforge.net/
Available on: Cheetah Cluster
Location: /opt/bio/emboss


FASTA

FASTA is a program used to search in large protein or DNA sequence data banks. See the Rocks Cluster Bio User Guide for simple instructions.

Software Homepage: http://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml
Available on: Cheetah Cluster
Location: /opt/bio/fasta/


Glimmer

Glimmer (Gene Locator and Interpolated Markov ModelER) is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. It uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. See the Rocks Cluster Bio User Guide for simple instructions.

Software Homepage: http://ccb.jhu.edu/software/glimmer/index.shtml
Available on: Cheetah Cluster
Location: /opt/bio/glimmer/


GROMACS

GROMACS (Groningen MAchine for Chemical Simulation) is a software suite meant for molecular dynamics simulation.

Software Homepage: http://www.gromacs.org/
Available on: Cheetah Cluster
Location: /opt/bio/gromacs


HMMER

HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using profile hidden Markov models (profile HMMs). See the Rocks Cluster Bio User Guide for simple instructions.

Software Homepage: http://hmmer.janelia.org/
Available on: Cheetah Cluster
Location: /opt/bio/hmmer


MrBayes

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. It uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters. See the Rocks Cluster Bio User Guide for simple instructions.

Software Homepage: http://mrbayes.sourceforge.net/
Available on: Cheetah Cluster
Command: mb
Location: /opt/bio/mrbayes


NCBI BLAST

BLAST (Basic Local Alignment Search Tool) is a collection of tools that are used to search for and find regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases, and calculates the statistical significance of the matches. This software suite has been released free to the public by the National Centre for Biotechnology Information.

Software Homepage: http://blast.ncbi.nlm.nih.gov/Blast.cgi
Available on: Cheetah Cluster
Location: /opt/bio/ncbi


PHYLIP

PHYLIP (Phylogeny Inference Package) is a package of programs for inferring phylogenies or evolutionary trees.

Software Homepage: http://evolution.genetics.washington.edu/phylip.html
Available on: Cheetah Cluster
Location: /opt/bio/phylip


T-Coffee

T-Coffee is a multiple sequence alignment package. It can align protein, DNA, and RNA sequences and is also able to combine sequence information with protein structural information, profile information, or RNA secondary structures.

Software Homepage: http://www.tcoffee.org/Projects/tcoffee/
Available on: Cheetah Cluster
Location: /opt/bio/tcoffee/