Generalized Mixture Models for Molecular Phylogenetic Estimation
نویسندگان
چکیده
منابع مشابه
Generalized mixture models for molecular phylogenetic estimation.
The rapidly growing availability of multigene sequence data during the past decade has enabled phylogeny estimation at phylogenomic scales. However, dealing with evolutionary process heterogeneity across the genome becomes increasingly challenging. Here we develop a mixture model approach that uses reversible jump Markov chain Monte Carlo (MCMC) estimation to permit as many distinct models as t...
متن کاملPhylogenetic mixture models for proteins.
Standard protein substitution models use a single amino acid replacement rate matrix that summarizes the biological, chemical and physical properties of amino acids. However, site evolution is highly heterogeneous and depends on many factors: genetic code; solvent exposure; secondary and tertiary structure; protein function; etc. These impact the substitution pattern and, in most cases, a singl...
متن کاملClassification of molecular sequence data using Bayesian phylogenetic mixture models
Rate variation among the sites of a molecular sequence is commonly found in applications of phylogenetic inference. Several approaches exist to account for this feature but they do not usually enable us to pinpoint the sites that evolve under one or another rate of evolution in a straightforward manner. In this paper we concentrate on phylogenetic mixture models as tools for site classification...
متن کاملEmpirical profile mixture models for phylogenetic reconstruction
MOTIVATION Previous studies have shown that accounting for site-specific amino acid replacement patterns using mixtures of stationary probability profiles offers a promising approach for improving the robustness of phylogenetic reconstructions in the presence of saturation. However, such profile mixture models were introduced only in a Bayesian context, and are not yet available in a maximum li...
متن کاملWhen do phylogenetic mixture models mimic other phylogenetic models?
Phylogenetic mixture models, in which the sites in sequences undergo different substitution processes along the same or different trees, allow the description of heterogeneous evolutionary processes. As data sets consisting of longer sequences become available, it is important to understand such models, for both theoretical insights and use in statistical analyses. Some recent articles have hig...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Systematic Biology
سال: 2011
ISSN: 1076-836X,1063-5157
DOI: 10.1093/sysbio/syr093