Cluster Software
Contents
- 1 Software on the Babylon Cluster
- 2 In /nfs/src
- 2.1 AMAP
- 2.2 BAli-Phy
- 2.3 BLAST
- 2.4 BLAT
- 2.5 CASA
- 2.6 Clustal W
- 2.7 CONTRAfold
- 2.8 DART
- 2.9 Exonerate
- 2.10 Foldalign and FoldalignM
- 2.11 GFF tools
- 2.12 Guile
- 2.13 HMMer
- 2.14 HMMoc
- 2.15 Infernal
- 2.16 MAFFT
- 2.17 makepp
- 2.18 MASTR
- 2.19 MAVID
- 2.20 Mercator
- 2.21 mpeg_encode
- 2.22 Murlet
- 2.23 MUSCLE
- 2.24 Ortheus
- 2.25 PAML
- 2.26 PECAN
- 2.27 PFOLD
- 2.28 PHAST
- 2.29 PHYLIP
- 2.30 PMARS
- 2.31 PROBCONS
- 2.32 Recodon
- 2.33 Repeatmasker
- 2.34 RNASampler
- 2.35 RNAz
- 2.36 SAPS
- 2.37 SNAP
- 2.38 Sun JDK
- 2.39 T-COFFEE
- 2.40 Vienna RNA
- 3 Elsewhere
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
- Numpy http://numpy.scipy.org/
- Rpy http://rpy.sourceforge.net/
- Py SQLdb http://sourceforge.net/projects/pysqldb
- Bio Python http://biopython.org/wiki/Main_Page
-- Ian Holmes - 18 Sep 2007
