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Methodologies for Phylogenetic Inference

Type of publication Peer-reviewed
Publikationsform Review article (peer-reviewed)
Author Gil Manuel, Anisimova Maria,
Project Fast joint estimation of alignment and phylogeny from genomic sequences in a frequentist framework
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Review article (peer-reviewed)

Journal eLS
Publisher Wiley Online Library
Page(s) 1 - 5
Title of proceedings eLS
DOI 10.1002/9780470015902.a0025545


Phylogenetic inference from homologous molecular sequences is key to hypothesis testing and problem solving not only in evolutionary biology but also in a wide variety of other fields – from medicine to ecology. Model-based phylogenetic methods rely on Markov substitution models to describe the molecular evolution as a stochastic process of character substitution over time on a phylogenetic tree relating the sequences. Model parameters are estimated with standard statistical inference methods, namely, Bayesian and maximum likelihood approaches. A typical phylogenetic analysis first infers a multiple sequence alignment. Given this alignment, a phylogenetic tree is then estimated togetherwith branch lengths and model parameters. Ideally, the alignment and phylogeny should be estimated simultaneously, amongst others to take alignment uncertainty into account.