Bioinformatic Resources
Our Favorites
HMMER - http://hmmer.org
SPIDEY :mRNA to genomic alignment
Multiple Alignment
EchinoDB :EchinoDB is a database consisting of amino acid sequence orthoclusters from 42 echinoderm transcriptomes.
Phylogenetic Analysis
Phylip 3.66:phylogenetic analysis
- Note: be sure to install libxaw7 and dev dbg headers packages before
compile 3.66;
- Note: This package is compiled from the latest version, not the EMBOSS
integrated phylip 3.6, which can be done by './configure --prefix=/usr/local'; not debian phylip 3.6.1.
Molphy 2.3b: Maximum Likelihood.
Tree-Puzzle 5.2: Maximum Likelihood.
Gene Prediction
GENSCAN
Note: The document can be found in /usr/local/share/genescan. Three trained models are available: HumanIso.smat, Arabidopsis.smat, Maize.smat.My personal experience is that Humalso is much better than other two for sea urchin.example: genscan /usr/local/share/genscan/HumanIso.smat mycontig.fasta
GlimmerHMM, 2.0.4
Note: The document can be found in /usr/local/share/GlimmerHMM. Two trained models are available: arabidopsis and rice. Not good for sea urchin. But user can train their own model. example: glimmerhmm
Contig600303.fasta –d /usr/local/share/GlimmerHMM/trained_dir/arabidopsis/
GeneZilla, 1.0, former TigerScan
Note: Only one model trained for human available now(/usr/local/share/genezilla). User has to go genezilla directory to run the program. example: ./genezilla human.iso ~/mycontig.fasta
Other bioinformatics software
Artemis 7:a DNA sequence viewer and annotation tool. Use 'art' to launch the artemis; use 'act' to launch ACT, a DNA sequence comparison viewer.
CD-HIT, v3.0.2(2006-0411) :CD-HI/CD-HIT clusters protein sequence database at high sequence identity threshold. This program can remove the high sequence redundancy
efficiently.
ViennaRNA : RNA Secondary Structure Prediction and Comparison.
RepeatMasker 3.2.8, with RepBase 20090604
Other Scientific Software
- R 2.9
- Gnuplot 4.2
- Grace 5.1.22
Programming Resources
- Python 2.3.5, BioPython 1.41
- Perl 5.16, BioPerl 1.4
- GCC 4.0.3
- J2SE 1.5
Credit: Original list compiled by Dr. Qiang Tu
Note: This page has been flagged as requiring an update as some software versions are now out of date.