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Locus-aware decomposition of gene trees with respect to polytomous species trees

Ciach, Michal and Muszewska, Anna and Górecki, Paweł (2018) Locus-aware decomposition of gene trees with respect to polytomous species trees. Algorithms for Molecular Biology . ISSN 1748-7188

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Abstract

Background: Horizontal gene transfer (HGT), a process of acquisition and fixation of foreign genetic material, is an important biological phenomenon. Several approaches to HGT inference have been proposed. However, most of them either rely on approximate, non-phylogenetic methods or on the tree reconciliation, which is computationally intensive and sensitive to parameter values. Results: We investigate the locus tree inference problem as a possible alternative that combines the advantages of both approaches. We present several algorithms to solve the problem in the parsimony framework. We introduce a novel tree mapping, which allows us to obtain a heuristic solution to the problems of locus tree inference and duplication classification. Conclusions: Our approach allows for faster comparisons of gene and species trees and improves known algorithms for duplication inference in the presence of polytomies in the species trees. We have implemented our algorithms in a software tool available at https ://githu b.com/mciac h/Locus TreeI nfere nce.

Item Type:Article
Subjects:Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Q Science > QA Mathematics > QA76 Computer software
Q Science > QR Microbiology
Divisions:Department of Microbial Biochemistry
ID Code:1537
Deposited By: dr Anna Muszewska
Deposited On:05 Jun 2018 08:03
Last Modified:05 Jun 2018 08:03

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