Datamonkey: rapid detection of selective pressure on individual sites of codon alignments
- PMID: 15713735
- DOI: 10.1093/bioinformatics/bti320
Datamonkey: rapid detection of selective pressure on individual sites of codon alignments
Abstract
Datamonkey is a web interface to a suite of cutting edge maximum likelihood-based tools for identification of sites subject to positive or negative selection. The methods range from very fast data exploration to the some of the most complex models available in public domain software, and are implemented to run in parallel on a cluster of computers.
Availability: http://www.datamonkey.org. In the future, we plan to expand the collection of available analytic tools, and provide a package for installation on other systems.
Similar articles
-
GARD: a genetic algorithm for recombination detection.Bioinformatics. 2006 Dec 15;22(24):3096-8. doi: 10.1093/bioinformatics/btl474. Epub 2006 Nov 16. Bioinformatics. 2006. PMID: 17110367
-
INCA: synonymous codon usage analysis and clustering by means of self-organizing map.Bioinformatics. 2004 Sep 22;20(14):2329-30. doi: 10.1093/bioinformatics/bth238. Epub 2004 Apr 1. Bioinformatics. 2004. PMID: 15059815
-
Malin: maximum likelihood analysis of intron evolution in eukaryotes.Bioinformatics. 2008 Jul 1;24(13):1538-9. doi: 10.1093/bioinformatics/btn226. Epub 2008 May 12. Bioinformatics. 2008. PMID: 18474506 Free PMC article.
-
Detecting signatures of selection from DNA sequences using Datamonkey.Methods Mol Biol. 2009;537:163-83. doi: 10.1007/978-1-59745-251-9_8. Methods Mol Biol. 2009. PMID: 19378144
-
An overview of the wcd EST clustering tool.Bioinformatics. 2008 Jul 1;24(13):1542-6. doi: 10.1093/bioinformatics/btn203. Epub 2008 May 14. Bioinformatics. 2008. PMID: 18480101 Free PMC article. Review.
Cited by
-
Molecular epidemiology and phylodynamics of the human respiratory syncytial virus fusion protein in northern Taiwan.PLoS One. 2013 May 29;8(5):e64012. doi: 10.1371/journal.pone.0064012. Print 2013. PLoS One. 2013. PMID: 23734183 Free PMC article.
-
Phylodynamic analysis of the canine distemper virus hemagglutinin gene.BMC Vet Res. 2015 Jul 25;11:164. doi: 10.1186/s12917-015-0491-9. BMC Vet Res. 2015. PMID: 26205391 Free PMC article.
-
Evolution of the voltage sensor domain of the voltage-sensitive phosphoinositide phosphatase VSP/TPTE suggests a role as a proton channel in eutherian mammals.Mol Biol Evol. 2012 Sep;29(9):2147-55. doi: 10.1093/molbev/mss083. Epub 2012 Mar 6. Mol Biol Evol. 2012. PMID: 22396523 Free PMC article.
-
Adaptive evolution and functional constraint at TLR4 during the secondary aquatic adaptation and diversification of cetaceans.BMC Evol Biol. 2012 Mar 24;12:39. doi: 10.1186/1471-2148-12-39. BMC Evol Biol. 2012. PMID: 22443485 Free PMC article.
-
Genetic structure of apical membrane antigen-1 in Plasmodium falciparum isolates from Pakistan.Parasites Hosts Dis. 2024 Aug;62(3):302-312. doi: 10.3347/PHD.24028. Epub 2024 Aug 26. Parasites Hosts Dis. 2024. PMID: 39218629 Free PMC article.
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources