List of packages installed on the HolmesLab cluster NFS.
Protein multiple alignment by sequence annealing. See the AMAP page.
MCMC Bayesian Alignment and Phylogeny estimation. Note: doesn't seem to run on sheridan for some reason - runs on cluster nodes ok.
Fast sequence homology search.
Fast(er) sequence homology search.
A hacked up version of AMAP for producing consensus alignments.
Aging but popular sequence alignment.
DNA, Amino acid & RNA Tests.
Multiple sequence StatisticalAlignment package.
StringTransducer visualization tool (see e.g. PhyloFilm).
RNA alignment & structure prediction.
Phylogenetic likelihood model for RNA structure evolution.
Dart perl scripts
Fast model-based sequence homology search.
Foldalign and FoldalignM
Havgaard and Gorodkin's RNA structural alignment programs.
Scripts for working with GFF format.
HiddenMarkovModel-based protein profiling & homology search tool used by the PfamDatabase.
GertonLunter's HMM compiler.
StochasticContextFreeGrammar-based RNA profiling & homology search tool used by the RfamDatabase.
Extensible GNU make clone.
Multi-genome progressive-Viterbi alignment.
RNA multiple alignment.
Phylogenetic sequence analysis.
See Ziheng Yang's PAML page at UCL.
Multi-genome consistency alignment.
CYK RNA structure prediction using KnudsenHein algorithm.
The PHAST package, including PhastCons, Exoniphy, etc.
Software package for inferring phylogenies.
RedCode interpreter for playing CoreWars.
ProbCons: multi-protein consistency alignment.
Coalescent simulations of DNA/codons with recombination, migration, and other options
Transposon and low-complexity repetitive sequence masking.
Only functional on lorien; needs Expect module installed (see RT #8)
StefanWashietl's software for noncoding RNA gene prediction.
Sequence analysis Perl modules.
The basis for the BDGP genome annotation pipeline.
IanKorf's software for protein-coding gene prediction.
64-bit Sun Java Development Kit/Runtime Environment.
The default java/gij install on most cluster nodes (notable exception: lorien) seem to be broken/lack necessary libraries. Use this instead.
Update: all active cluster nodes now have the jdk installed as the default in alternatives. Theoretically, /usr/bin/java will run /nfs/src/jdk1.6.0_04/jre/bin/java from now on. More information here.
Progressive consistency-based alignment. See the manual.
Ivo Hofacker's ViennaRNA package (version 1.7).
Sun Grid Engine
-- IanHolmes - 18 Sep 2007