Bioinformatics Software

BLAST
BLAST (Basic Local Alignment Search Tool) is a sequence similarity search tool. BLAST can align both nucleotide and protein sequences to identify homologous relationships. It uses a pairwise, heuristic algorithm to search for matching local regions rather than performing a global alignment across the entire sequence. This gives BLAST a significant speed advantage over alternative algorithms and has helped to make it the most widespread sequence analysis software used in the biosciences today. Access is provided through the SAPAC BLAST Portal.

CCP4
The UK based Collaborative Computer Project 4 is a protein crystallography software suite. It contains a large range of programs that communicate between shared data formats. Programs include data processing for raw reflection files, data combination and scaling, molecular averaging, molecular replacement, coordinate analysis, map manipulation and model refinement.

ClustalW
ClustalW is a progressive multiple sequence alignment program. It searches for the best global alignment, the best match over the entire length of the sequences. ClustalW is progressive, it performs a series of steps in order to increase performance. ClustalW first builds a pairwise distance matrix of the sequences, then creates a guide tree from which the alignment proceeds. This directed alignment (ClustalW first aligns sequences closest together on the tree) greatly improves the speed of results. ClustalW is used to infer homology and evolutionary relationships. ClustalW is located at /opt/shared/clustalw on Hydra. Instruction for submitting job on Hydra are available here. ClustalW documentation is available here.

CNS
The Crystallography & NMR System is a program that provides a computational framework for the structural determination of macromolecules by X-Ray Crystallography and solution NMR. CNS provides modules that assists in all stages of the determination process, such as procedures for phasing and refinement of crystallography data and the capacity to perform operations on data structures like electron density maps. CNS also provides a high level language for the development of your own algorithms within the CNS framework.

Last Modified: 6 December, 2004
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HMMer
HMMer is a sensitive, position specific protein sequence analysis program. It creates and uses Profile Hidden Markov Models which statistically describe conserved regions of protein sequence (motifs) generated from multiple sequence alignments (unaligned sequences can be used but this is less effective). Profiles can be used to query a sequence database to find homologous matches. HMMer can also search a Profile database given a sequence file as input and perform multiple sequence alignments using Profiles and sequence files. HMMer is located at /opt/shared/hmmer on Hydra. Instruction for submitting job on Hydra are available here. The HMMer user guide is available here.

MrBayes
MrBayes is a program for applying Bayesian inference to a phylogeny. Bayesian inference is a statistical technique that takes into account prior knowledge into an inference or an estimation. MrBayes uses the Metropolis-Hastings algorithm, a Markov Chain Monte Carlo method, to calculate the Bayesian inference of a phylogenetic tree space so that the optimum phylogeny can be chosen. MrBayes receives a phylogeny in the NEXUS format and provide a file of the sample trees and second file containing their parameters as output. MrBayes is located at /opt/shared/local/bin/mb on Hydra. Instruction for submitting job on Hydra are available here. The MrBayes manual can be downloaded here.

PHYLIP
PHYLIP (PHYlogeny Inference Package) is a suite of programs for inferring phylogenetic relationships. It is a comprehensive package and through its components is able to analyse DNA and protein sequences, distance matrices, restriction sites or fragments, discrete characters and gene frequencies. Many different statistical methods are available including parsimony, distance matrix and likelihood. Along with the commercial package, PAUP*, PHYLIP is responsible for the majority of published phylogenetic trees.