Global alignment of molecular sequences via ancestral state reconstruction

Alexandr Andoni, Constantinos Daskalakis, Avinatan Hassidim and Sebastien Roch

Stochastic Processes and their Applications, 2012, vol. 122, issue 12, 3852-3874

Abstract: We consider the trace reconstruction problem on a tree (TRPT): a binary sequence is broadcast through a tree channel where we allow substitutions, deletions, and insertions; we seek to reconstruct the original sequence from the sequences received at the leaves. The TRPT is motivated by the multiple sequence alignment problem in computational biology. We give a simple recursive procedure giving strong reconstruction guarantees at low mutation rates. To our knowledge, this is the first rigorous trace reconstruction result on a tree in the presence of indels.

Keywords: Markov models on trees; Branching processes; Phylogenetic inference (search for similar items in EconPapers)
Date: 2012
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DOI: 10.1016/j.spa.2012.08.004

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