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

By Sergei L. Kosakovsky Pond, Simon D. W. Frost. Bioinform., 2005

1,375 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2f0620074d4ff4f58329bda434980c0e0a2a1644

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In Molecular Biology

Citations in the corpus

Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models (2008, methodology): “Pre-processing of uploaded alignments (supporting NEXUS, PHYLIP, MEGA, and FASTA formats), estimation of tree topology, and MPI-enabled model selection and nucleotide and codon model fitting are handled using modified pre-existing scripts in the Datamonkey system ( Kosakovsky Pond and Frost (2005a) ”
Not so different after all: a comparison of methods for detecting amino acid sites under selection. (2005, methodology): “All sequence manipulations and analyses were performed with the HyPhy software package (Kosakovsky Pond, Frost, and Muse 2005).”
Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach (2007, methodology): “For instance, The SNAP server (15) is based on counting methods which estimate the number of synonymous and non-synonymous substitutions between all pairs of sequences (19,20), and the Data-Monkey server ( 16 ) is based on a combination of model hypothesis testing and codon ancestral sequence recons”