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

Constantinos Daskalakis; Sebastien Roch

doi:10.1214/12-aap852

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arXiv · 1109.5002

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

Constantinos Daskalakis·Sebastien Roch

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Abstract

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.

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BibTeX RIS

Constantinos Daskalakis, Sebastien Roch. 2011-09-23. Alignment-free phylogenetic reconstruction: Sample complexity via a branching process analysis. https://doi.org/10.1214/12-aap852

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