IDEA: Interactive Display for Evolutionary Analyses

IDEA (Interactive Display for Evolutionary Analyses) is a graphical interface for PAML (Yang, Z., 1997), a popular package for conducting molecular evolution analyses on phylogenies and associated sequences. IDEA’s organized parameter-entry interface for codeml and baseml prevents common errors and adds options to reconstruct phylogenetic trees using PhyML (Guindon, S., Gascuel, O., 2003) or PHYLIP (Felsenstein, J., 1989) and to combine the results of repeated analyses for increased accuracy. Many datasets may be analyzed in parallel. IDEA’s output display for codeml analyses of sites-based evolutionary models features an interactive tabular summary of results, visualizations of selective pressure along genes, interactive histograms and depictions of phylogenetic trees with branch lengths proportional to the estimated number of nucleotide substitutions.



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System Requirements