Datamonkey 2010: a suite of phylogenetic analysis tools.
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To perform a selection analysis, datamonkey.org needs a multiple alignment of at least three homologous coding nucleotide sequences. Codon based methods for estimating dN and dS can be applied to any sequence alignment, but there are several considerations to keep in mind.
Datamonkey. A Collection of State of the Art Statistical Models and Bioinformatics Tools.
The Datamonkey and HyPhy team is working on the initiative to address the COVID-19 pandemic - read more at covid19.datamonkey.org Datamonkey Adaptive Evolution Server Methods and Tools.
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If you publish the results based on Datamonkey.org we suggest the following citations. Please cite the Datamonkey and HyPhy application notes: Datamonkey webserver Wayne Delport, Art F. Poon, Simon D. W. Frost and Sergei L. Kosakovsky Pond Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology.
Summary: Datamonkey is a popular web-based suite of phylogenetic analysis tools for use in evolutionary biology. Since the original release in 2005, we have expanded the analysis options to include recently developed algorithmic methods for recombination detection, evolutionary fingerprinting of genes, codon model selection, co-evolution between sites, identification of sites, which rapidly.
Summary: 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.
Lab Report 2 CSB352: Lab Report 2 Objective: Perform a phylogenetic analysis on your subset of BLAST hits from At4g28230 generating the best-resolved phylogenetic tree you can. In addition, perform Datamonkey analysis on the sequence set, and determine what kind of selection (or lack thereof) is acting on the orthologs.
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Different types of models are used in Datamonkey and other selection analysis from BIOLOGY PUBLIC at The City College of New York, CUNY.
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