Cluster Software

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Software on the Babylon Cluster

List of packages installed on the Holmes Lab 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.

  • BLAST

BLAT

Fast(er) sequence homology search.

  • BLAT

CASA

A hacked up version of AMAP for producing consensus alignments.

Clustal W

Aging but popular sequence alignment.

CONTRAfold

DART

DNA, Amino acid & RNA Tests.

XRate

Phylo Grammar engine.

Handel

Multiple sequence Statistical Alignment package.

Phylocomposer

Transducer Composition software.

Phylodirector

String Transducer visualization tool (see e.g. Phylo Film).

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

Hidden Markov Model-based protein profiling & homology search tool used by the Pfam Database.

HMMoc

Gerton Lunter's HMM compiler.

Infernal

Stochastic Context Free Grammar-based RNA profiling & homology search tool used by the Rfam Database.

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 Knudsen Hein algorithm.

PHAST

The PHAST package, including Phast Cons, Exoniphy, etc.

PHYLIP

Software package for inferring phylogenies.

PMARS

Red Code interpreter for playing Core Wars. 8-)

PROBCONS

Prob Cons: 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

Stefan Washietl's software for noncoding RNA gene prediction.

SAPS

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

SNAP

Ian Korf'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.

Vienna RNA

Ivo Hofacker's Vienna RNA package (version 1.7).

Elsewhere

Sun Grid Engine

Bioperl

My SQL

Python Packages

-- Ian Holmes - 18 Sep 2007