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  CSM Computational Biology Software

There are two broad categories of computational biology software available through the CSM Laboratory -- bioinformatics applications and all others.

 

Bioinformatics Software

The following is a partial list of bioinformatics software available through the iNquiry interface installed on the hhmibio cluster. In fact, many more packages are available and the list is constantly expanding, so please go to our local iNquiry page to see the full selection of bioinformatics applications. The iNquiry page also inlcudes more detailed infomation about each application. (Note that you will need a login name and password to access the iNquiry page. If you do not have one, simply request one by submitting a CSM work-order.)

EMBOSS - A high-quality package of free, Open Source software for molecular biology

BLAST - Various forms provided by the BioTeam & NCBI.

Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.

Clustalw is a general purpose multiple sequence alignment program for DNA or proteins.

PHYLIP is a free package of programs for inferring phylogenies.

HMMER - Profile hidden Markov models (profile HMMs) can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis.

mpiBLAST is a freely available, open-source parallelization of BLAST.

PAUP is a software package for inference of evolutionary trees.

Wise2 compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.

MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. This package is also available on the Curie cluster.

MODELLER is a computer program that models three-dimensional structures of proteins and their assemblies by satisfaction of spatial restraints. Modeller is available on the Curie cluster.

 

Other Software

AMBER - Assisted Model Building and Energy Refinement is a suite of tools for building, running, and analyzing a variety of molecular dynamics-based calculations.

CHARMM - Chemistry at HARvard Macromolecular Mechanics is a suite of tools for building, running, and analyzing a variety of molecular dynamics-based calculations.

Matlab - A powerful computing environment for numeric computation, algorithm development, data visualization, and data analysis.