The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics.

From 138662 embryophyte (higher plant) and 348142 chordate genes, 4216 embryophyte and 15452 chordate gene families were generated. For each of these gene families, multiple sequence alignments, phylogenetic trees, ratios of non-synonymous to synonymous nucleotide substitution rates (Ka/Ks), mappings from gene trees to the NCBI taxonomy and structural links to solved three-dimensional protein structures in the Protein Data Bank (PDB) with Grantham-weightedmutationalfactorswereallcalculated. Ofthe‘gene family trees’,173 embryophyteand 505 chordate branches show Ka/Ks 1 and are candidates for functional adaptation. The calculated information is available both as a gene family database and as a phylogenetically indexed resource, called ‘The Adaptive Evolution Database’ (TAED), available at http://www.bioinfo.no/tools/TAED.