Alignment-Free phylogenetic reconstruction
RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
Fast and reliable reconstruction of phylogenetic trees with indistinguishable edges
Random Structures & Algorithms
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We introduce a new distance-based phylogeny reconstruction technique which provably achieves, at sufficiently short branch lengths, a sequence length requirement growing slower than any polynomial. The technique is based on a new averaging procedure that implicitly reconstructs ancestral sequences.In the same token, we extend previous results on phase transitions in phylogeny reconstruction to general time-reversible models. More precisely, we show that in the so-called Kesten-Stigum zone---roughly, a region of the parameter space where ancestral sequences are well approximated by ``linear combinations'' of observed sequences---sequences of length $e^{\sqrt{\log n}}$ suffice for reconstruction. Here $n$ is the number of extant species. We improve this result to $\poly(\log n)$in the ultrametric case. Surprisingly, this last result suggests that a UPGMA-type algorithm may in some sense be ``optimal'' under a molecular clock.Our results challenge---to some extent---the conventional wisdom that estimates of evolutionary distances alone carry significantly less information about phylogenies than full sequence datasets.