EvolMAP is an algorithm and software for estimating the composition of ancestral genomes and the timing of gene duplication and loss events. The input is a species-tree and genes from its modern species. The output is the inferred ancestral genes of the speciation nodes of the tree and the inferred gene duplication & loss events specific to each branch. EvolMAP features include:

• Detection of orthologous groups from an ancestral gene perspective (i.e. descendants of an ancestral gene)
• Scalable and fast genome-level comparisons laying out timings of gene duplications and losses
• Generating gene expansion (GE) tree which is useful to track evolution of a specific domain on the species tree
• Generating average ortholog divergence (AOD) tree which is a measure of the molecular clock
• Categorizing divergence of gene duplications into in-paralogs, diverged in-paralogs and ambiguous gains

Onur Sakarya, Kenneth S. Kosik and Todd H. Oakley. Reconstructing ancestral genome content based on symmetrical best alignments and Dollo parsimony. Bioinformatics 2008 24(5):606-612.

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