Wikiomics:Phylogenetic databases


 * PhyloFacts The PhyloFacts resource provides multiple sequence alignments, phylogenetic trees, hidden Markov models, predicted 3D structures, predicted subfamilies and annotation data for protein families across the Tree of Life. PhyloFacts currently has >40K protein family "books", some of which are constructed for individual protein structure domains, while the majority represent proteins clustered into global homology groups (proteins sharing the same domain architecture). This second type of clustering allows biologists to infer a molecular function (and possible cellular role) for proteins. Data can be downloaded from the resource, and sequences can be submitted for classification to families and subfamilies.
 * Tree of Life A huge resource of phylogenetic information.
 * TreeBase is a relational database storing phylogenetic trees and the data matrices used to generate them from published research papers.
 * TreeFam is a database of phylogenetic trees of animal genes. It aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene families.