PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment.

By Nicolas Lartillot, Nicolas Rodrigue, Daniel M. Stubbs, J. Richer. Systematic Biology, 2013

809 citations recorded by the source corpus.

Subfields: Artificial Intelligence, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e6b5a6d94f418a194edc28fdd259e106596520e6

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Citations in the corpus

OMA standalone: orthology inference among public and custom genomes and transcriptomes (2018, methodology): “tracted to the long branched Nematoda—a problem to which PhyloBayes under the CAT model has been previously shown to be more robust (Lartillot et al. 2013).”
Phylotranscriptomic analysis of the origin and early diversification of land plants (2014, methodology): “The extensively trimmed amino acid and nucleotide supermatrices were analyzed with the site-heterogeneous CAT+Gamma model using PhyloBayes MPI (118).”
Pitfalls in supermatrix phylogenomics (2017, positive): “Posterior predictive tests as implemented in programs such as PhyloBayes 3 (Lartillot et al. 2013) and PHYCAS (Lewis et al. 2015) allow evaluation of model fi t to the data or part of the data.”
Selecting optimal partitioning schemes for phylogenomic datasets (2014, background): “Some approaches automatically assign sites to different substitution models (e.g. [ 15,16]), and others estimate more than one model of molecular evolution for each site (e.g. [ 17-19]).”
Higher‐level phylogeny and evolutionary history of Pentatomomorpha (Hemiptera: Heteroptera) inferred from mitochondrial genome sequences (2019, methodology): “5a (Lartillot et al., 2013), with a maximum parsimony (MP) method using tnt v.”
Mutational effects on stability are largely conserved during protein evolution (2013, background): “Such models use various approaches: sites can be preassigned equilibrium frequencies based on structural features (21–23), or modeling with force fields (19, 20), sites can be allowed to choose among a predefined set of equilibrium frequencies (17, 18), or the equilibrium frequencies can themselves ”
Structural Insight into How Bacteria Prevent Interference between Multiple Divergent Type IV Secretion Systems (2015, methodology): “2e (75) under the CAT-GTR model, with the bipartition frequencies analyzed at various time points using the bpcomp program.”
Higher‐level phylogeny of longhorn beetles (Coleoptera: Chrysomeloidea) inferred from mitochondrial genomes (2020, methodology): “5a (Lartillot et al., 2013), and under maximum likelihood (ML) optimization using RAxML (Stamatakis et al., 2008).”