title: A daily-updated tree of (sequenced) life as a reference for genome research.
abstract: We report a daily-updated sequenced/species Tree Of Life (sTOL) as a reference for the increasing number of cellular organisms with their genomes sequenced. The sTOL builds on a likelihood-based weight calibration algorithm to consolidate NCBI taxonomy information in concert with unbiased sampling of molecular characters from whole genomes of all sequenced organisms. Via quantifying the extent of agreement between taxonomic and molecular data, we observe there are many potential improvements that can be made to the status quo classification, particularly in the Fungi kingdom; we also see that the current state of many animal genomes is rather poor. To augment the use of sTOL in providing evolutionary contexts, we integrate an ontology infrastructure and demonstrate its utility for evolutionary understanding on: nuclear receptors, stem cells and eukaryotic genomes. The sTOL (http://supfam.org/SUPERFAMILY/sTOL) provides a binary tree of (sequenced) life, and contributes to an analytical platform linking genome evolution, function and phenotype.
authors.affiliation: Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK.
authors.forename: Hai
authors.initials: H
authors.lastname: Fang
authors.forename: Matt E
authors.initials: ME
authors.lastname: Oates
authors.forename: Ralph B
authors.initials: RB
authors.lastname: Pethica
authors.forename: Jenny M
authors.initials: JM
authors.lastname: Greenwood
authors.forename: Adam J
authors.initials: AJ
authors.lastname: Sardar
authors.forename: Owen J L
authors.initials: OJ
authors.lastname: Rackham
authors.forename: Philip C J
authors.initials: PC
authors.lastname: Donoghue
authors.forename: Alexandros
authors.initials: A
authors.lastname: Stamatakis
authors.forename: David A
authors.initials: DA
authors.lastname: de Lima Morais
authors.forename: Julian
authors.initials: J
authors.lastname: Gough
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic / Q000592:standards; D016678:Genome; D023281:Genomics / Q000379:methods / Q000592:standards; D020407:Internet; D010802:Phylogeny