Population & Evolutionary Genomics - Tools
IDEA (Interactive Display for Evolutionary Analyses) provides a graphical interface for PAML (Phylogenetic Analysis by Maximum Likelihood, Ziheng Yang, 1997), a suite of programs for conducting molecular evolution analyses on nucleotide and amino-acid data. IDEA allows you to run either of the PAML programs codeml or baseml on a single dataset or on multiple datasets simultaneously. Among other things, codeml and baseml allow you to obtain maximum likelihood estimates of numbers of substitutions per branch and per site and to compare multiple models of molecular evolution given the data and a phylogenetic tree for the sequences. IDEA runs on Linux, Solaris and Mac OS X operating systems; it is designed to execute processes in parallel on a multiprocessor machine and can run on a computer grid with either SGE or Condor. IDEA is available free of charge from SourceForge.