The Adaptive Evolution Database (TAED)
This site will be the future home of TAED. A new release is expected in Spring, 2011. The current status of the updated project is that initial families are being reconstructed following All vs. All BLAST and alignment quality control steps. Multiple sequence alignment and phylogenetic tree construction for gene families is onging. Updated information will be released as it becomes available.
When released, TAED will contain gene families with the last common ancestor of Chordates maximally as the oldest node, multiple sequence alignments, maximum likelihood phylogenetic trees, ancestral sequences at each node, dN/dS and amino acid rate shifts calculated along each branch, gene tree/species tree reconciliation to map each gene tree branch to one or more species tree branches, searches enabled by gene family or species tree lineage, and mapping of substitutions onto 3D protein structures where close homologs are available in PDB. The database will be automatically updated.
Together with the TAED database, we expect to release software for 3D phylogenetic tree visualization and for gene tree/species tree reconciliation (both parsimony and model-based).
Flat files from the release described in Roth et al. (2005), Nucleic Acids Research 33:D495-D497 can be downloaded from: http://www.wyomingbioinformatics.org/~chregu/more_pages/Research.htm.
The database described in Liberles et al. (2001) Genome Biology 2(8):research0028 can be accessed from : http://www.sbc.su.se/~liberles/TAED3.0/2index.html