Identifiability and inference of non-parametric rates-across-sites models on large-scale phylo\-genies
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Abstract: Mutation rate variation across loci is well known to cause difficulties, notably identifiability issues, in the reconstruction of evolutionary trees from molecular sequences. Here we introduce a new approach for estimating general rates-across-sites models. Our results imply, in particular, that large phylogenies are typically identifiable under rate variation. We also derive sequence-length requirements for high-probability reconstruction. Our main contribution is a novel algorithm that clusters sites according to their mutation rate. Following this site clustering step, standard reconstruction techniques can be used to recover the phylogeny. Our results rely on a basic insight: that, for large trees, certain site statistics experience concentration-of-measure phenomena.
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Cites work
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(10)- Analytic solutions for three taxon ML trees with variable rates across sites
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- Reversible polymorphism-aware phylogenetic models and their application to tree inference
- Counting mutations by parsimony and estimation of mutation rate variation across nucleotide sites -- a simulation study
- Identifiability and inference of phylogenetic birth-death models
- Consistency and identifiability of the polymorphism-aware phylogenetic models
- Phase transition in the sample complexity of likelihood-based phylogeny inference
- Full reconstruction of non-stationary strand-symmetric models on rooted phylogenies
- Identifiability of a Markovian model of molecular evolution with gamma-distributed rates
- Continuous and tractable models for the variation of evolutionary rates
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