IDEA: Interactive Display for Evolutionary Analyses

Background: The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other molecular evolution variables of interest an increasingly important approach to addressing broad evolutionary questions. Two of the programs most widely used for this purpose are codeml and baseml, parts of the PAML (Phylogenetic Analysis by Maximum Likelihood) suite. A significant drawback of these programs is their lack of a graphical user interface, which can limit their user base and considerably reduce their efficiency. Results: We have developed IDEA (Interactive Display for Evolutionary Analyses), an intuitive graphical input and output interface which interacts with PHYLIP for phylogeny reconstruction and with codeml and baseml for molecular evolution analyses. IDEA's graphical input and visualization interfaces eliminate the need to edit and parse text input and output files, reducing ...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Amy Egan, Anup Mahurkar, Jonathan Crabtree, Jonathan H. Badger, Jane M. Carlton, Joana C. Silva
• Keywords: BMCBI 2008, Graphical User Interface, Molecular Evolution, Selective Constraints