Prospects for building the tree of life from large sequence databases.
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.
Driskell
Amy C
AC
Section of Evolution and Ecology, University of California, One Shields Avenue, Davis, CA 95616, USA. acdriskell@ucdavis.edu
Ané
Cécile
C
Burleigh
J Gordon
JG
McMahon
Michelle M
MM
O'meara
Brian C
BC
Sanderson
Michael J
MJ
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
D010940:Plant Proteins