ArticleMolecular biology and evolution2015
Maximum-Likelihood Tree Estimation Using Codon Substitution Models with Multiple Partitions.
Article in Molecular biology and evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
6 citing papers in PubMed.
- MixtureFinder: Estimating DNA Mixture Models for Phylogenetic Analyses.Molecular biology and evolution · 2025Article
- Next-generation development and application of codon model in evolution.Frontiers in genetics · 2023Review
- Marginal diversity analysis of conservation of Chinese domestic duck breeds.Scientific reports · 2019Article
- Big data analysis of human mitochondrial DNA substitution models: a regression approach.BMC genomics · 2018Article
- Microbial sequence typing in the genomic era.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2018Review
- Trends in substitution models of molecular evolution.Frontiers in genetics · 2015Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Many protein sequences have distinct domains that evolve with different rates, different selective pressures, or may differ in codon bias. Instead of modeling these differences by more and more complex models of molecular evolution, we present a multipartition approach that allows maximum-likelihood phylogeny inference using different codon models at predefined partitions in the data. Partition models can, but do not have to, share free parameters in the estimation process. We test this approach with simulated data as well as in a phylogenetic study of the origin of the leucin-rich repeat regions in the type III effector proteins of the pythopathogenic bacteria Ralstonia solanacearum. Our study does not only show that a simple two-partition model resolves the phylogeny better than a one-partition model but also gives more evidence supporting the hypothesis of lateral gene transfer events between the bacterial pathogens and its eukaryotic hosts.
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