Counting, generating and sampling tree alignments

Cedric Chauve 1 Julien Courtiel 1 Yann Ponty 2, 3
3 AMIB - Algorithms and Models for Integrative Biology
LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau], LRI - Laboratoire de Recherche en Informatique, UP11 - Université Paris-Sud - Paris 11, Inria Saclay - Ile de France
Abstract : Pairwise ordered tree alignment are combinatorial objects that appear in important applications, such as RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical sets of matches between identical pairs of trees. This ambiguity is uninforma-tive, and detrimental to any probabilistic analysis. In this work, we consider tree alignments up to equivalence. Our first result is a precise asymptotic enumeration of tree alignments, obtained from a context-free grammar by mean of basic analytic combinatorics. Our second result focuses on alignments between two given ordered trees S and T. By refining our grammar to align specific trees, we obtain a decomposition scheme for the space of alignments, and use it to design an efficient dynamic programming algorithm for sampling alignments under the Gibbs-Boltzmann probability distribution. This generalizes existing tree alignment algorithms, and opens the door for a probabilistic analysis of the space of suboptimal alignments.
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https://hal.inria.fr/hal-01154030
Contributor : Yann Ponty <>
Submitted on : Saturday, December 12, 2015 - 10:53:28 AM
Last modification on : Wednesday, March 27, 2019 - 4:41:29 PM
Long-term archiving on : Saturday, April 29, 2017 - 11:44:23 AM

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  • HAL Id : hal-01154030, version 2
  • ARXIV : 1505.05983

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Cedric Chauve, Julien Courtiel, Yann Ponty. Counting, generating and sampling tree alignments. ALCOB - 3rd International Conference on Algorithms for Computational Biology - 2016, Jun 2016, Trujillo, Spain. ⟨hal-01154030v2⟩

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