Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs.

ABSTRACT: Here, we constructed a phylogenetic tree of 17 bacterial phyla covering eubacteria and archaea by using a new method and 102 carefully selected orthologs from their genomes. One of the serious disturbing factors in phylogeny construction is the existence of out-paralogs that cannot easily be found out and discarded. In our method, out-paralogs are detected and removed by constructing a phylogenetic tree of the genes in question and examining the clustered genes in the tree. We also developed a method for comparing two tree topologies or shapes, ComTree. Applying ComTree to the constructed tree we computed the relative number of orthologs that support a node of the tree. This number is called the Positive Ortholog Ratio (POR), which is conceptually and methodologically different from the fr

SUBMITTER: Horiike T 

PROVIDER: S-EPMC2648810 | biostudies-literature | 2009 Jan

REPOSITORIES: biostudies-literature