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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Isometric gene tree reconciliation revisited.

Broňa Brejová1, Askar Gafurov1, Dana Pardubská1

  • 1Faculty of Mathematics, Physics, and Informatics, Comenius University, Mlynská dolina, 842 48 Bratislava, Slovakia.

Algorithms for Molecular Biology : AMB
|June 21, 2017
PubMed
Summary
This summary is machine-generated.

This study corrects an isometric gene tree reconciliation algorithm, improving its accuracy and efficiency. New methods are presented for tree reconciliation, addressing evolutionary history reconstruction.

Keywords:
Gene family evolutionGene tree reconciliationLevel ancestor

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Isometric gene tree reconciliation, introduced by Ma et al. in 2008, addresses gene tree/species tree reconciliation while respecting branch lengths.
  • This problem is relevant for reconstructing evolutionary histories of genomes under the infinite sites model.

Purpose of the Study:

  • To identify and correct inaccuracies in the original isometric gene tree reconciliation algorithm.
  • To improve the computational efficiency of the reconciliation process.
  • To explore new variants of tree reconciliation, including unrooted trees and branch length scaling.

Main Methods:

  • Modification of the existing isometric gene tree reconciliation algorithm by Ma et al.
  • Development of new algorithms for tree reconciliation problems.
  • Analysis of computational complexity and running time improvements.

Main Results:

  • The original algorithm by Ma et al. was found to be incorrect.
  • A modified, corrected algorithm was proposed.
  • Running time was improved from O(N^3) to O(N^2), where N is the total number of nodes.
  • Two new variants of the problem were examined: reconciliation of unrooted trees and scaling of gene tree branch lengths.

Conclusions:

  • Several new algorithms for isometric tree reconciliation have been developed.
  • Open questions remain, particularly regarding extensions for imprecise branch length estimates.