Computational protocol: The Tree and Net Components of Prokaryote Evolution

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[…] We analyzed the set of 6,901 phylogenetic trees from () that were obtained using the following methodology (supplementary fig. S1, Supplementary Material online). Clusters of orthologous genes were obtained from the COG (; ) and eggNOG () databases from 100 prokaryotic species (59 bacteria and 41 archaea). The species were manually selected to represent the diversity of the taxonomy in prokaryotes (the complete list of species is given in supplementary table S1, Supplementary Material online). The BeTs algorithm () was used to identify those orthologs with the highest sequence conservation, so the final clusters have a maximum of 100 species, with no more than one representative of each species. All clusters were aligned using the program Muscle () with default parameters. Alignments were refined with the Gblocks program () with the minimal length of a block set at six amino acid positions, and the maximum number of allowed contiguous nonconserved amino acid positions set at 20. The program Multiphyl (), which selects the best of 88 amino acid substitution models, was used to reconstruct the maximum likelihood (ML) tree of each cluster. The NUTs are defined as trees from COGs that are represented in more than 90% of the species included in the study (supplementary table S2, Supplementary Material online). […]

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