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Software on the BabylonCluster

List of packages installed on the HolmesLab cluster NFS.

In /nfs/src

AMAP

Protein multiple alignment by sequence annealing. See the AMAP page.

BAli-Phy

MCMC Bayesian Alignment and Phylogeny estimation. Note: doesn't seem to run on sheridan for some reason - runs on cluster nodes ok.

BLAST

Fast sequence homology search.

BLAT

Fast(er) sequence homology search.

CASA

A hacked up version of AMAP for producing consensus alignments.

ClustalW

Aging but popular sequence alignment.

CONTRAfold

DART

DNA, Amino acid & RNA Tests.

XRate

PhyloGrammar engine.

Handel

Multiple sequence StatisticalAlignment package.

Phylocomposer

TransducerComposition software.

Phylodirector

StringTransducer visualization tool (see e.g. PhyloFilm).

Stemloc

RNA alignment & structure prediction.

Evoldoer

Phylogenetic likelihood model for RNA structure evolution.

Dart perl scripts

Exonerate

Fast model-based sequence homology search.

Foldalign and FoldalignM

Havgaard and Gorodkin's RNA structural alignment programs.

GFF tools

Scripts for working with GFF format.

Guile

HMMer

HiddenMarkovModel-based protein profiling & homology search tool used by the PfamDatabase.

HMMoc

GertonLunter's HMM compiler.

Infernal

StochasticContextFreeGrammar-based RNA profiling & homology search tool used by the RfamDatabase.

MAFFT

makepp

Extensible GNU make clone.

MASTR

MAVID

Multi-genome progressive-Viterbi alignment.

Mercator

mpeg_encode

Make movies!

Murlet

RNA multiple alignment.

MUSCLE

Multiple alignment.

Ortheus

PAML

Phylogenetic sequence analysis.

See Ziheng Yang's PAML page at UCL.

PECAN

Multi-genome consistency alignment.

PFOLD

CYK RNA structure prediction using KnudsenHein algorithm.

PHAST

The PHAST package, including PhastCons, Exoniphy, etc.

PHYLIP

Software package for inferring phylogenies.

PMARS

RedCode interpreter for playing CoreWars. cool!

PROBCONS

ProbCons: multi-protein consistency alignment.

Recodon

Coalescent simulations of DNA/codons with recombination, migration, and other options

Repeatmasker

Transposon and low-complexity repetitive sequence masking.

RNASampler

Only functional on lorien; needs Expect module installed (see RT #8)

RNAz

StefanWashietl's software for noncoding RNA gene prediction.

SAPS

Sequence analysis Perl modules. The basis for the BDGP genome annotation pipeline.

SNAP

IanKorf's software for protein-coding gene prediction.

Sun JDK

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.

/nfs/src/jdk1.6.0_04/jre/bin/java

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.

T-COFFEE

Progressive consistency-based alignment. See the manual.

ViennaRNA

Ivo Hofacker's ViennaRNA package (version 1.7).

Elsewhere

Sun Grid Engine

Bioperl

MySQL

Python Packages

-- IanHolmes - 18 Sep 2007

Topic revision: r65 - 2010-09-09 - IanHolmes
 

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