Algorithms for MDC-based multi-locus phylogeny inference: beyond rooted binary gene trees on single alleles.

Content Provider	Europe PMC
Author	Yu, Yun Warnow, Tandy Nakhleh, Luay
Copyright Year	2011
Abstract	Abstract One of the criteria for inferring a species tree from a collection of gene trees, when gene tree incongruence is assumed to be due to incomplete lineage sorting (ILS), is Minimize Deep Coalescence (MDC). Exact algorithms for inferring the species tree from rooted, binary trees under MDC were recently introduced. Nevertheless, in phylogenetic analyses of biological data sets, estimated gene trees may differ from true gene trees, be incompletely resolved, and not necessarily rooted. In this article, we propose new MDC formulations for the cases where the gene trees are unrooted/binary, rooted/non-binary, and unrooted/non-binary. Further, we prove structural theorems that allow us to extend the algorithms for the rooted/binary gene tree case to these cases in a straightforward manner. In addition, we devise MDC-based algorithms for cases when multiple alleles per species may be sampled. We study the performance of these methods in coalescent-based computer simulations.
Related Links	https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3216099&blobtype=pdf
Page Count	17
ISSN	10665277
Volume Number	18
DOI	10.1089/cmb.2011.0174
PubMed Central reference number	PMC3216099
Issue Number	11
PubMed reference number	22035329
Journal	Journal of Computational Biology [J Comput Biol]
e-ISSN	15578666
Language	English
Publisher	Mary Ann Liebert, Inc.
Publisher Date	2011-10-28
Publisher Place	USA
Access Restriction	Open
Rights License	Copyright 2011, Mary Ann Liebert, Inc.
Subject Keyword	algorithms coalescence dynamic programming graph theory phylogenetic trees
Content Type	Text
Resource Type	Article
Subject	Genetics Molecular Biology Computational Theory and Mathematics Modeling and Simulation Computational Mathematics