Alignment-free phylogenetic reconstruction: Sample complexity via a branching process analysis

Alignment-free phylogenetic reconstruction: Sample complexity via a branching process analysis

We present an efficient phylogenetic reconstruction algorithm allowing insertions and deletions which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa. Our algorithm is distance-based, that is, it relies on pairwise sequence comparison...

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Bibliographic Details
Main Authors: Roch, Sebastien (Author), Daskalakis, Konstantinos (Contributor)
Other Authors: Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science (Contributor)
Format: Article
Language:English
Published: Institute of Mathematical Statistics, 2015-11-20T18:15:30Z.
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Summary:We present an efficient phylogenetic reconstruction algorithm allowing insertions and deletions which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa. Our algorithm is distance-based, that is, it relies on pairwise sequence comparisons. More importantly, our approach largely bypasses the difficult problem of multiple sequence alignment.
Alfred P. Sloan Foundation (Fellowship)
National Science Foundation (U.S.) (CAREER Award CCF-0953960)
National Science Foundation (U.S.) (Award CCF-1101491)

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