Computational protocol: Rooting the Domain Archaea by Phylogenomic Analysis Supports the Foundation of the New Kingdom Proteoarchaeota

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Protocol publication

[…] Sets of homologous protein sequences were aligned using MAFFT with default parameters (). Conserved positions in the alignments were detected using BMGE with default parameters and the BLOSUM62 substitution matrix, which represents a good compromise between too stringent and too relaxed matrices to deal with sequences with a large range of similarity values as in the case of global archaeal phylogenies (). The trimmed alignments were verified by hand using the program NET of the MUST package (). Maximum-likelihood (ML) phylogenetic trees were reconstructed upon each individual protein or different concatenated data sets with RaxML v.7.2.4 () and the PROTGAMMALGF model. Tree robustness was estimated using the Rapid Bootstrapping method implemented in RaxML. Bayesian inference analyses were carried out using MrBayes 3.2.1 () with a mixed model of amino acid sequence evolution and a Gamma distribution with six discrete categories to accommodate for among site rate variation. Four independent chains were run for 2,000,000 generations and trees sampled every 100 trees. To construct a majority rule consensus tree, the first 5,000 trees were eliminated as burn-in. […]

Pipeline specifications

Software tools MAFFT, BMGE, RAxML, MrBayes
Application Phylogenetics