Isometric gene tree reconciliation revisited.

Broňa Brejová, Askar Gafurov, Dana Pardubská, Michal Sabo, Tomáš Vinař

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Article in Algorithms for molecular biology : AMB, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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5 · Who and what money

Authors and funding

5 authors.

Broňa BrejováFaculty of Mathematics, Physics, and Informatics, Comenius University, Mlynská dolina, 842 48 Bratislava, Slovakia.

Askar GafurovFaculty of Mathematics, Physics, and Informatics, Comenius University, Mlynská dolina, 842 48 Bratislava, Slovakia.

Dana PardubskáFaculty of Mathematics, Physics, and Informatics, Comenius University, Mlynská dolina, 842 48 Bratislava, Slovakia.

Michal SaboFaculty of Mathematics, Physics, and Informatics, Comenius University, Mlynská dolina, 842 48 Bratislava, Slovakia.

Tomáš VinařFaculty of Mathematics, Physics, and Informatics, Comenius University, Mlynská dolina, 842 48 Bratislava, Slovakia.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundIsometric 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. in 2008 in the context of reconstructing evolutionary histories of genomes in the infinite sites model.

resultsIn 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. We have also improved the running time from [Formula: see text] to [Formula: see text], where

conclusionsWe provide several new algorithms for isometric reconciliation of trees. Some questions in this area remain open; most importantly extensions of the problem allowing for imprecise estimates of branch lengths.

Indexed as

Gene family evolutionGene tree reconciliationLevel ancestor

Identifiers

PMID28630644

DOI10.1186/s13015-017-0108-x

PMCPMC5470333

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LicenceCC BY

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.