title: Prospects for building the tree of life from large sequence databases.
abstract: We assess the phylogenetic potential of approximately 300,000 protein sequences sampled from Swiss-Prot and GenBank. Although only a small subset of these data was potentially phylogenetically informative, this subset retained a substantial fraction of the original taxonomic diversity. Sampling biases in the databases necessitate building phylogenetic data sets that have large numbers of missing entries. However, an analysis of two "supermatrices" suggests that even data sets with as much as 92% missing data can provide insights into broad sections of the tree of life.
authors.affiliation: Section of Evolution and Ecology, University of California, One Shields Avenue, Davis, CA 95616, USA. acdriskell@ucdavis.edu
authors.forename: Amy C
authors.initials: AC
authors.lastname: Driskell
authors.forename: Cécile
authors.initials: C
authors.lastname: Ané
authors.forename: J Gordon
authors.initials: JG
authors.lastname: Burleigh
authors.forename: Michelle M
authors.initials: MM
authors.lastname: McMahon
authors.forename: Brian C
authors.initials: BC
authors.lastname: O'meara
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Sanderson
mesh_terms: D000818:Animals; D000852:Anopheles / Q000145:classification / Q000235:genetics; D044822:Biodiversity; D005075:Biological Evolution; D002965:Classification; D019295:Computational Biology; D030561:Databases, Nucleic Acid; D030562:Databases, Protein; D005810:Multigene Family; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D010944:Plants / Q000145:classification / Q000235:genetics; D018411:Spodoptera / Q000145:classification / Q000235:genetics
chemical_list: D010940:Plant Proteins