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

TLDR

Datamonkey is a popular web‑based suite of phylogenetic analysis tools used in evolutionary biology. This paper summarizes the current analysis options available on Datamonkey and provides guidelines for their use in evolutionary biology. The suite now includes expanded options such as recombination detection, evolutionary fingerprinting, codon‑model selection, co‑evolution analysis, site identification for immune escape, HIV‑1 subtype assignment, and updated selection tools. The suite is available at http://www.datamonkey.org.

Abstract

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 escape host-immune pressure and HIV-1 subtype assignment. The traditional selection tools have also been augmented to include recent developments in the field. Here, we summarize the analyses options currently available on Datamonkey, and provide guidelines for their use in evolutionary biology. Availability and documentation: http://www.datamonkey.org.