Broňa Brejová, Askar Gafurov, Dana Pardubská, Michal Sabo, Tomáš Vinař. Isometric Gene Tree Reconciliation Revisited. In Martin Frith, Christian Nørgaard Storm Pedersen, ed., Algorithms in Bioinformatics (WABI), 9838 volume of Lecture Notes in Computer Science, pp. 40-51, Aarhus, Denmark, 2016. Springer.

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Isometric gene tree reconciliation is a gene tree / species tree
reconciliation problem where both the gene tree and the species tree include branch lengths, and these branch lengths must be respected by the
reconciliation. The problem was introduced by Ma et al. 2008 in the
context of reconstructing evolutionary histories of genomes in
infinite sites model. In this paper, we show that the original
algorithm by Ma et al. is incorrect, and we propose a modified
algorithm that addresses the problems that we discovered. Moreover, by
adapting a data structure by Amir et al. 2007, we were able to improve
running time from O(mn) to O(n+mlog m), where n is the size of
the species tree, and m is the size of the gene tree.