Identifiability and inference of non-parametric rates-across-sites models on large-scale phylogenies
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.
Keywords
Cite
@article{arxiv.1108.0129,
title = {Identifiability and inference of non-parametric rates-across-sites models on large-scale phylogenies},
author = {Elchanan Mossel and Sebastien Roch},
journal= {arXiv preprint arXiv:1108.0129},
year = {2011}
}