PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

Abstract

We propose a software package, PhyloBayes 3, which can be used for conducting Bayesian phylogenetic reconstruction and molecular dating analyses, using a large variety of amino acid replacement and nucleotide substitution models, including empirical mixtures or non-parametric models, as well as alternative clock relaxation processes.

Gene duplication, loss and selection in the evolution of saxitoxin biosynthesis in alveolates

“…Maximum Likelihood (ML) analyses were performed with RAxML-VI-HPCv8.0.0, GTRCAT model with 25 rate categories (Stamatakis, 2006). Bayesian inference was carried out using Phylobayes v3.3f (Lartillot et al, 2009) under the GTRCAT substitution model with a free number of mixing categories and a discrete across site variation under 4 categories. Trees were inferred when the largest maximum difference between the bipartitions (chains) was <0.1.…”

“…The most likely topology was established from 100 separate searches, and bootstrap analyses were performed with 1000 pseudoreplicates. Bayesian inference was carried out using Phylobayes v3.3f (Lartillot et al, 2009) under the LGCAT substitution model, as previously described. All model estimation and phylogenetic analyses were done using either Lifeportal (https://lifeportal.uio.no) or the abel server at the University of Oslo.…”

Re-evaluating the phylogeny of Sipuncula through transcriptomics

“…The first 2,500 trees (25%) were discarded as burn-in for each MCMC run prior to convergence (i.e., when maximum discrepancies across chains < 0.1). The small dataset (constructed with ortholog groups containing 13 or more taxa) was subjected to additional Bayesian analyses in PhyloBayes (Lartillot et al, 2009) using the CAT-GTR mixture model (Lartillot and Philippe, 2004) and two independent Markov chains. Convergence was tested using the ''bpcomp'' program in the PhyloBayes suite.…”

Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon Protocruzia and unravels the deep phylogenetic affinities of the ciliate lineages

“…The Bayesian Inference (BI) trees were generated for the midsize dataset using the program PhyloBayes-MPI 1.4e with the CAT-GTR model + C distribution (Lartillot et al, 2009). Four independent chains were run for 20,000 generations (convergence Maxdiff = 0.00996335 with 10% burn-in).…”

“…Therefore, it is more likely that the differences in the two topologies are due to the phylogenetic models used in our ML (LG model) and BI (CAT model) analyses. Several recent studies that involve large datasets have shown that the CAT model is better fitting and more biologically realistic than LG (Brown et al, in press;Burki et al, 2013;Lartillot et al, 2009). Thus, the topology derived from the BI analysis is in all likelihood the most accurate.…”