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Title: Bayesian evolutionary model testing in the phylogenomics era: matching model complexity with computational efficiency
Authors: Baele, Guy ×
Lemey, Philippe #
Issue Date: Aug-2013
Publisher: Oxford University Press
Series Title: Bioinformatics vol:29 issue:16 pages:1970-1979
Article number: 10.1093/bioinformatics/btt340
Abstract: The advent of new sequencing technologies has led to increasing amounts of data being available to perform phylogenetic analyses, with genomic data giving rise to the field of phylogenomics. High-performance computing is becoming an indispensable research tool to fit complex evolutionary models, which take into account specific genomic properties, to large datasets. Here, we perform an extensive Bayesian phylogenetic model selection study, comparing codon and nucleotide substitution models, including codon position partitioning for nucleotide data as well gene-specific substitution models for both data types. For the best fitting partitioned models, we also compare independent partitioning with standard diffuse prior specification to conditional partitioning via hierarchical prior specification. To compare the different models, we use state-of-the-art marginal likelihood estimation techniques, including path sampling and stepping-stone sampling.
URI: 
ISSN: 1367-4803
Publication status: published
KU Leuven publication type: IT
Appears in Collections:Laboratory of Clinical and Epidemiological Virology (Rega Institute)
× corresponding author
# (joint) last author

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