PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

Abstract

Modeling across site variation of the substitution process is increasingly recognized as important for obtaining more accurate phylogenetic reconstructions. Both finite and infinite mixture models have been proposed and have been shown to significantly improve on classical single-matrix models. Compared with their finite counterparts, infinite mixtures have a greater expressivity. However, they are computationally more challenging. This has resulted in practical compromises in the design of infinite mixture models. In particular, a fast but simplified version of a Dirichlet process model over equilibrium frequency profiles implemented in PhyloBayes has often been used in recent phylogenomics studies, while more refined model structures, more realistic and empirically more fit, have been practically out of reach. We introduce a message passing interface version of PhyloBayes, implementing the Dirichlet process mixture models as well as more classical empirical matrices and finite mixtures. The parallelization is made efficient thanks to the combination of two algorithmic strategies: a partial Gibbs sampling update of the tree topology and the use of a truncated stick-breaking representation for the Dirichlet process prior. The implementation shows close to linear gains in computational speed for up to 64 cores, thus allowing faster phylogenetic reconstruction under complex mixture models. PhyloBayes MPI is freely available from our website www.phylobayes.org.

Evolutionary origin of a streamlined marine bacterioplankton lineage

“…As expected, the RAxML software (Stamatakis, 2014) clustered SAR11 and Rickettsiales at the base of the tree (Supplementary Figure S1), but this clustering had less statistical support (Supplementary Figure S1) compared with that of the RAxML tree based solely on the 24 heterogeneous proteins (Figure 2b), as a result of conflicting phylogenetic signals contained in the two protein subsets. Intriguingly, the CAT model (Lartillot and Philippe, 2004) in the PhyloBayes MPI software (Lartillot et al, 2013) yielded a phylogeny (Supplementary Figure S2) displaying an identical topology to the RAxML tree (Supplementary Figure S1), which is at odds with the previous PhyloBayes analyses that were based on concatenated data sets that, although distinct from this 52-protein data set, also consist of both composition-homogeneous and heterogeneous protein sequences (Viklund et al, 2012;Luo et al, 2013;Viklund et al, 2013); these previous analyses placed SAR11 in the middle of the non-endosymbiotic lineages (Figures 1c and d). The P4 Bayesian software offers the NDCH model that allows the amino acid composition to vary across lineages (Foster, 2004).…”

“…Phylogenomic tree reconstruction using a Bayesian mixture model Among-site compositional heterogeneity was accounted for by the CAT Bayesian mixture model (Lartillot and Philippe, 2004) implemented in the PhyloBayes MPI software package (Lartillot et al, 2013). The Bayesian MCMC analyses were run with CAT-GTR model with a Gamma distribution of rates among sites using the concatenated datasets of the 52 protein sequences.…”

Genomic data do not support comb jellies as the sister group to all other animals

“…Model Testing. We used Bayesian cross-validation (36,37) implemented in PhyloBayes 3.3 (59) to compare the fit of the site-homogeneous WAG and GTR models and the site-heterogeneous CAT and CAT-GTR models (20,22). To alleviate computational burden, we restricted these analyses to three exemplar datasets: Ryan-Choano, Moroz-3D, and Whelan-6-Choano.…”

“…Ryan-Choano was also analyzed under CAT-GTR. All CAT and CAT-GTR analyses were performed using PhyloBayes MPI 1.5a (59). We analyzed Moroz-3D in RAxML 8.0.26 (60) using WAG (20) and LG (44) with empirical amino acid frequencies (+F), as well as under CAT-GTR with PhyloBayes MPI.…”

The complete mitogenome of the trilobite beetle, Platerodrilus sp. (Elateroidea: Lycidae)

“…We performed a Bayesian inference as implemented in PhyloBayes MPI 1.5a (Lartillot et al 2013) using the site-heterogeneous mixture CAT-GTR model (Lartillot & Philippe 2004). The newly determined mitogenome sequence was aligned in Translator X (Abascal et al 2010) with orthologous sequences corresponding to complete or nearly complete mitogenomes available in GenBank for Elateroidea and closely related superfamilies with Scirtoidea as outgroup.…”