Specs
IBM p550 Power5 9133-55A
4 x dual-core POWER5+ 1.9Ghz
8GB RAM
8x73GB SCSI HD's in RAID5

Operating System
Gentoo Linux

Access
This system is currently in use by the Gentoo Linux PPC64 team. Access is handled by them.

HMMER v2.3.2 AltiVec Generation 2 with modification for better performance.

HMMER2.3.2 AltiVec Generation 2 with modification

This release of Clustalw allows the Clustalw to be executed on the Cell processor, on the PS3 and/or on the Cell blade.

PROBCONS is a novel tool for generating multiple alignments of protein sequences. Using a combination of probabilistic modeling and consistency-based alignment techniques, PROBCONS has achieved the highest accuracy of all alignment methods to date. The executable of this package ProbCons v1.11 is built on IBM eServer BladeCenter JS20 system running SUSE SLES9 using IBM XL C/C++ compiler version 7. The binaries are suitable for execution on systems with POWER4, POWER5 and PPC970 processors.

X! tandem is an open source software that can model mass spectra with protein sequences. The executable in this package of X! tandem (tandem-linux-06-09-15-3) is built on IBM eServer BladeCenter JS20 system running SUSE SLES9 using IBM XL C/C++ compiler version 7. The binaries are suitable for execution on POWER4, POWER5 and PPC970 processors.

MODELTEST is program for the selection the model of nucleotide substitution that best fits the data. The program chooses among 56 models, and implements three different model selection frameworks: hierarchical likelihood ratio tests (hLRTs), Akaike information criterion (AIC), and Bayesian information criterion (BIC). The program also implements the assesment of model uncertainty and tools for model averaging and calculation of parameter importance, using the AIC or the BIC.

T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can combine sequences and structures.

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.

Bioconductor (http://www.bioconductor.org) is an open source project for the analysis and comprehension of genomic data and developed by the Fred Hutchinson Cancer Research Center and various US & international institutions. Bioconductor is based on the R programming language. There are two releases of Bioconductor every year (they appear shortly after the corresponding R release). At any one time there is a release version, which corresponds to the released version of R, and a development version, which corresponds to the development version of R. Most users will find the release version appropriate for their needs.