PAUP is a leading program for performing phylogenetic analysis for bioinformatics sequences. PAUP currently runs as a single processor program. No further enhancements are suggested.
Bioinformatics & Biology
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. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees.
LS-DYNA is a general purpose finite element code for simulating complex structural problems, specializing in nonlinear, transient dynamic problems using explicit integration. LS-DYNA is one of the codes developed at Livermore Software Technology Corporation (LSTC).
Profile hidden Markov models (profile HMMs) can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus. HMMER uses profile HMMs, and can be useful in situations like:
- if you are working with an evolutionarily diverse protein family, a BLAST search with any individual sequence may not find the rest of the sequences in the family.
- the top hits in a BLAST search are hypothetical sequences from genome projects.
- your protein consists of several domains which are of different types.
HMMER (pronounced 'hammer', as in a more precise mining tool than BLAST) was developed by Sean Eddy at Washington University in St. Louis.
HMMER is a very cpu-intensive program and is parallelized using threads, so that each instance of hmmsearch or the other search programs can use all the cpus available on a node. HMMER on OSC clusters are intended for those who need to run HMMER searches on large numbers of query sequences.
EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole.
Within EMBOSS you will find around hundreds of programs (applications) covering areas such as:
- Sequence alignment,
- Rapid database searching with sequence patterns,
- Protein motif identification, including domain analysis,
- Nucleotide sequence pattern analysis---for example to identify CpG islands or repeats,
- Codon usage analysis for small genomes,
- Rapid identification of sequence patterns in large scale sequence sets,
- Presentation tools for publication
Clustal W is a general purpose multiple sequence alignment program for DNA or proteins.It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen.
BLAT is a sequence analysis tool which performs rapid mRNA/DNA and cross-species protein alignments. BLAT is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences.
BLAT is not BLAST. DNA BLAT works by keeping an index of the entire genome (but not the genome itself) in memory. Since the index takes up a bit less than a gigabyte of RAM, BLAT can deliver high performance on a reasonably priced Linux box. The index is used to find areas of probable homology, which are then loaded into memory for a detailed alignment. Protein BLAT works in a similar manner, except with 4-mers rather than 11-mers. The protein index takes a little more than 2 gigabytes.
The BLAST programs are widely used tools for searching DNA and protein databases for sequence similarity to identify homologs to a query sequence. While often referred to as just "BLAST", this can really be thought of as a set of programs: blastp, blastn, blastx, tblastn, and tblastx.
Bioperl offers a set of perl modules which can be used for sequence manipulation. Knowledge of PERL programming is required.
The Assisted Model Building with Energy Refinement (AMBER) package contains many molecular simulation programs targeted at biomolecular systems. A wide variety of modelling techniques are available. It generally scales well on modest numbers of processors, and the GPU enabled CUDA programs are very efficient.
Availability and Restrictions
AMBER is available on Ruby, Oakley, and Glenn Clusters. The following versions are currently available at OSC (S means serial executables, P means parallel, and C means CUDA, i.e., GPU enabled):