List of packages installed on the HolmesLab
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
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
-based protein profiling & homology search tool used by the PfamDatabase
's HMM compiler.
-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
package, including PhastCons
, Exoniphy, etc.
Software package for inferring phylogenies.
interpreter for playing CoreWars
: 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)
's software for noncoding RNA gene prediction.
Sequence analysis Perl modules.
The basis for the BDGP
genome annotation pipeline.
'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
- 18 Sep 2007