TreeBASE Search-Analyses for study 15140

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Analyses for Study 15140

Citation title: "Codon-based phylogenetics introduces novel flagellar gene markers to oomycete systematics".

Study name: "Codon-based phylogenetics introduces novel flagellar gene markers to oomycete systematics".

This study is part of submission 15140 (Status: Published).

Analysis details

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We used the site-heterogeneous mutation-selection model based on the Dirichlet process (Rodrigue et al., 2010), implemented in the MPI version of PhyloBayes (Lartillot et al., 2013; Rodrigue and Lartillot, 2013) to infer the phylogeny based on the concatenation of the PF16 and OCM1 genes. We ran two independent Markov chain Monte Carlo calculations for 11,000 cycles (each including multiple updates on the tree topology, branch lengths, and substitution model parameters), discarded the first 1,000 draws as burn-in, and used the remaining to obtain the 60% consensus tree. The maxdiff score (Lartillot et al., 2009) obtained from the two chains was ~ 0.2, indicating that they had reached reasonable convergence

Output data

Analysis details

Name

Input data

Analysis step

Step details

Name

Software used

Name
Version
URL
Algorithm
Commands
We used the site-heterogeneous mutation-selection model based on the Dirichlet process (Rodrigue et al., 2010), implemented in the MPI version of PhyloBayes (Lartillot et al., 2013; Rodrigue and Lartillot, 2013) to infer the phylogeny based on the concatenation of the PF16 and OCM1 genes. We ran two independent Markov chain Monte Carlo calculations for 11,000 cycles (each including multiple updates on the tree topology, branch lengths, and substitution model parameters), discarded the first 1,000 draws as burn-in, and used the remaining to obtain the 60% consensus tree. The maxdiff score (Lartillot et al., 2009) obtained from the two chains was ~ 0.2, indicating that they had reached reasonable convergence

Output data