Treerecs: an integrated phylogenetic tool, from sequences to reconciliations

Nicolas Comte; Benoit Morel; Damir Hasić; Laurent Guéguen; Bastien Boussau; Vincent Daubin; Simon Penel; Celine Scornavacca; Manolo Gouy; Alexandros Stamatakis; Eric Tannier; David P Parsons

doi:10.1093/bioinformatics/btaa615

Treerecs: an integrated phylogenetic tool, from sequences to reconciliations

Bioinformatics. 2020 Sep 15;36(18):4822-4824. doi: 10.1093/bioinformatics/btaa615.

Authors

Nicolas Comte¹, Benoit Morel², Damir Hasić³, Laurent Guéguen⁴, Bastien Boussau⁴, Vincent Daubin⁴, Simon Penel⁴, Celine Scornavacca⁵, Manolo Gouy⁴, Alexandros Stamatakis^{2

6}, Eric Tannier^{1

4}, David P Parsons¹

Affiliations

¹ Inria Grenoble Rhône-Alpes, 38334 Montbonnot, France.
² Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.
³ Department of Mathematics, University of Sarajevo, Sarajevo, Bosnia and Herzegovina.
⁴ Université de Lyon, Laboratoire de Biométrie et Biologie Évolutive, CNRS UMR5558, F-69622 Villeurbanne, France.
⁵ ISEM, CNRS, Université de Montpellier, IRD, EPHE, Montpellier 34000, France.
⁶ Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany.

PMID: 33085745
DOI: 10.1093/bioinformatics/btaa615

Abstract

Motivation: Gene and species tree reconciliation methods are used to interpret gene trees, root them and correct uncertainties that are due to scarcity of signal in multiple sequence alignments. So far, reconciliation tools have not been integrated in standard phylogenetic software and they either lack performance on certain functions, or usability for biologists.

Results: We present Treerecs, a phylogenetic software based on duplication-loss reconciliation. Treerecs is simple to install and to use. It is fast and versatile, has a graphic output, and can be used along with methods for phylogenetic inference on multiple alignments like PLL and Seaview.

Availability and implementation: Treerecs is open-source. Its source code (C++, AGPLv3) and manuals are available from https://project.inria.fr/treerecs/.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Evolution, Molecular*
Phylogeny
Sequence Alignment
Software