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• W2019933943 abstract "Over 3000 microbial (bacterial and archaeal) genomes have been made publically available to date, providing an unprecedented opportunity to examine evolutionary genomic trends and offering valuable reference data for a variety of other studies such as metagenomics. The utility of these genome sequences is greatly enhanced when we have an understanding of how they are phylogenetically related to each other. Therefore, we here describe our efforts to reconstruct the phylogeny of all available bacterial and archaeal genomes. We identified 24, single-copy, ubiquitous genes suitable for this phylogenetic analysis. We used two approaches to combine the data for the 24 genes. First, we concatenated alignments of all genes into a single alignment from which a Maximum Likelihood (ML) tree was inferred using RAxML. Second, we used a relatively new approach to combining gene data, Bayesian Concordance Analysis (BCA), as implemented in the BUCKy software, in which the results of 24 single-gene phylogenetic analyses are used to generate a “primary concordance” tree. A comparison of the concatenated ML tree and the primary concordance (BUCKy) tree reveals that the two approaches give similar results, relative to a phylogenetic tree inferred from the 16S rRNA gene. After comparing the results and the methods used, we conclude that the current best approach for generating a single phylogenetic tree, suitable for use as a reference phylogeny for comparative analyses, is to perform a maximum likelihood analysis of a concatenated alignment of conserved, single-copy genes." @default.
• W2019933943 created "2016-06-24" @default.
• W2019933943 creator A5047169338 @default.
• W2019933943 creator A5059066311 @default.
• W2019933943 creator A5086404955 @default.
• W2019933943 date "2013-04-25" @default.
• W2019933943 modified "2023-09-27" @default.
• W2019933943 title "Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices" @default.
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• W2019933943 doi "https://doi.org/10.1371/journal.pone.0062510" @default.
• W2019933943 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/3636077" @default.
• W2019933943 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/23638103" @default.
• W2019933943 hasPublicationYear "2013" @default.
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