Designing fast converging phylogenetic methods

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Designing fast converging phylogenetic methods (2001)

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by Luay Nakhleh , Usman Roshan , Katherine St. John , Jerry Sun , Tandy Warnow

Venue:	IN PROC. 9TH INT’L CONF. ON INTELLIGENT SYSTEMS FOR MOLECULAR BIOLOGY (ISMB’01), VOLUME 17 OF BIOINFORMATICS
Citations:	6 - 1 self

BibTeX

@INPROCEEDINGS{Nakhleh01designingfast,
    author = {Luay Nakhleh and Usman Roshan and Katherine St. John and Jerry Sun and Tandy Warnow},
    title = {Designing fast converging phylogenetic methods},
    booktitle = {IN PROC. 9TH INT’L CONF. ON INTELLIGENT SYSTEMS FOR MOLECULAR BIOLOGY (ISMB’01), VOLUME 17 OF BIOINFORMATICS},
    year = {2001},
    pages = {190--198},
    publisher = {Oxford U. Press}
}

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Abstract

Absolute fast converging phylogenetic reconstruction methods are provably guaranteed to recover the true tree with high probability from sequences that grow only polynomially in the number of leaves, once the edge lengths are bounded arbitrarily from above and below. Only a few methods have been determined to be absolute fast converging; these have all been developed in just the last few years, and most are polynomial time. In this paper, we compare pre-existing fast converging methods as well as some new polynomial time methods that we have developed. Our study, based upon simulating evolution under a wide range of model conditions, establishes that our new methods outperform both neighbor joining and the previous fast converging methods, returning very accurate large trees, when these other methods do poorly.

Keyphrases

phylogenetic method new polynomial time method neighbor joining new method phylogenetic reconstruction method absolute fast converging wide range polynomial time high probability previous fast accurate large tree true tree last year edge length model condition

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