Date of this Version
Journal of Mathematical Biology
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.
The final publication is available at Springer via http://dx.doi.org/ 10.1007/s00285-012-0571-4.
phylogenetic reconstruction, rates-across-sites models, concentration of measure
Mossel, E., & Roch, S. (2013). Identifiability and Inference of Non-Parametric Rates-Across-Sites Models on Large-Scale Phylogenies. Journal of Mathematical Biology, 67 (4), 767-797. http://dx.doi.org/10.1007/s00285-012-0571-4
Date Posted: 27 November 2017
This document has been peer reviewed.