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Literature DB >> 15713735

Datamonkey: rapid detection of selective pressure on individual sites of codon alignments.

Sergei L Kosakovsky Pond¹, Simon D W Frost.

Abstract

UNLABELLED: 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.

Mesh：

Substances：
Codon

Year: 2005 PMID： 15713735 DOI： 10.1093/bioinformatics/bti320

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

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Cited

602 in total

1. Detection of minority resistance during early HIV-1 infection: natural variation and spurious detection rather than transmission and evolution of multiple viral variants.

Authors: Sara Gianella; Wayne Delport; Mary E Pacold; Jason A Young; Jun Yong Choi; Susan J Little; Douglas D Richman; Sergei L Kosakovsky Pond; Davey M Smith
Journal: J Virol Date: 2011-06-01 Impact factor: 5.103

Datamonkey: rapid detection of selective pressure on individual sites of codon alignments.

1. Detection of minority resistance during early HIV-1 infection: natural variation and spurious detection rather than transmission and evolution of multiple viral variants.

2. Determinants of the DNA binding specificity of class I and class II TCP transcription factors.

3. Genome-wide networks of amino acid covariances are common among viruses.

4. Nature and intensity of selection pressure on CRISPR-associated genes.

5. Evolution and adaptation of hemagglutinin gene of human H5N1 influenza virus.

6. Level of gene expression is a major determinant of protein evolution in the viral order Mononegavirales.

7. Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology.

8. Multi-year evolutionary dynamics of West Nile virus in suburban Chicago, USA, 2005-2007.

9. Long-term evolution of the Luteoviridae: time scale and mode of virus speciation.

10. A history of recurrent positive selection at the toll-like receptor 5 in primates.