imported>Ctelmer |
imported>BArsh |
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| ===== Our Favorites =====
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| [http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI BLAST]
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| [http://emboss.sourceforge.net/ EMBOSS]
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| [http://hmmer.org/ HMMER]
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| [http://www.ncbi.nlm.nih.gov/spidey/ SPIDEY] :mRNA to genomic alignment
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| ===== Multiple Alignment =====
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| [http://www.ebi.ac.uk/Tools/msa/clustalw2/ ClustalW2]
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| [http://www.tcoffee.org/ T_Coffee]
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| [http://doua.prabi.fr/software/seaview Seaview:alignment editor]
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| ===== Phylogenetic Analysis =====
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| [http://evolution.genetics.washington.edu/phylip.html Phylip 3.66:phylogenetic analysis]
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| * Note: be sure to install libxaw7 and dev dbg headers packages before<br />
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| compile 3.66;
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| * Note: This package is compiled from the latest version, not the EMBOSS<br />
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| integrated phylip 3.6, which can be done by './configure --prefix=/usr/local'; not debian phylip 3.6.1.
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| Molphy 2.3b: Maximum Likelihood.
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| Tree-Puzzle 5.2: Maximum Likelihood.
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| [http://doua.prabi.fr/software/njplot NJplot tree drawing]
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| ===== Gene Prediction =====
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| [http://genes.mit.edu/GENSCAN.html GENSCAN]<br />
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| 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
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| [https://ccb.jhu.edu/software/glimmerhmm/ GlimmerHMM, 2.0.4]<br />
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| 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<br />
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| Contig600303.fasta –d /usr/local/share/GlimmerHMM/trained_dir/arabidopsis/
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| [http://www.genezilla.org/ GeneZilla, 1.0, former TigerScan]<br />
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| 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
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| ===== Other bioinformatics software =====
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| [http://bioinfo.ut.ee/primer3-0.4.0/ Primer 3, Release 1.0]
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| [http://www.sanger.ac.uk/science/tools/artemis 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.
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| [http://bioinformatics.org/cd-hit/ 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<br />
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| efficiently.
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| [http://www.tbi.univie.ac.at/RNA/ ViennaRNA] : RNA Secondary Structure Prediction and Comparison.
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| [http://www.repeatmasker.org/ RepeatMasker 3.2.8, with RepBase 20090604]
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| ===== Other Scientific Software =====
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| * R 2.9
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| * Gnuplot 4.2
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| * Grace 5.1.22
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| ===== Programming Resources =====
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| * Python 2.3.5, BioPython 1.41
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| * Perl 5.16, BioPerl 1.4
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| * GCC 4.0.3
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| * J2SE 1.5
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| Credit: Original list compiled by Dr. Qiang Tu<br/>
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| Note: This page has been flagged as requiring an update as some software versions are now out of date.
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