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IDEA: Interactive Display for Evolutionary Analyses

Amy Egan1, Anup Mahurkar1, Jonathan Crabtree1, Jonathan H Badger2, Jane M Carlton3 and Joana C Silva14*

Author Affiliations

1 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA

2 The J. Craig Venter Institute, San Diego, CA 92121, USA

3 Department of Medical Parasitology, New York University School of Medicine, New York, NY 10010, USA

4 Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA

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BMC Bioinformatics 2008, 9:524  doi:10.1186/1471-2105-9-524

Published: 8 December 2008



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.


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 the likelihood of errors and improving processing time. Further, its interactive output display gives the user immediate access to results. Finally, IDEA can process data in parallel on a local machine or computing grid, allowing genome-wide analyses to be completed quickly.


IDEA provides a graphical user interface that allows the user to follow a codeml or baseml analysis from parameter input through to the exploration of results. Novel options streamline the analysis process, and post-analysis visualization of phylogenies, evolutionary rates and selective constraint along protein sequences simplifies the interpretation of results. The integration of these functions into a single tool eliminates the need for lengthy data handling and parsing, significantly expediting access to global patterns in the data.