Reconciling gene trees to a species tree

Authors:
Paola Bonizzoni;Gianluca Della Vedova;Riccardo Dondi
Affiliations:
Dipartimento di Informatica, Sistemistica e Comunicazione, Università degli Studi di Milano-Bicocca, Milano, Italy;Dipartimento di Statistica Università degli Studi di Milano-Bicocca, Milano, Italy;Dipartimento di Informatica, Sistemistica e Comunicazione, Università degli Studi di Milano-Bicocca, Milano, Italy
Venue:
CIAC'03 Proceedings of the 5th Italian conference on Algorithms and complexity
Year:
2003

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Abstract

In this paper we deal with the general problem of recombining the information from evolutionary trees representing the relationships between distinct gene families. First we solve a problem from [8] regarding the construction of a minimum reconciled tree by giving an efficient algorithm. Then we show that the exemplar problem, arising from the exemplar analysis of multigene genomes [2], is NP-hard even when the number of copies of a given label is at most two. Finally we introduce two novel formulations for the problem of recombining evolutionary trees, extending the notion of the gene duplication problem studied in [8,11,9,10,6], and we give an exact algorithm (via dynamic programming) for one of the formulations given.