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Treerecs: an integrated phylogenetic tool, from sequences to reconciliations.

Nicolas Comte 1 Benoît Morel 2 Damir Hasic 3 Laurent Guéguen 4 Bastien Boussau 4 Vincent Daubin 4 Simon Penel 4 Celine Scornavacca 5 Manolo Gouy 4 Alexandros Stamatakis 2, 6 Eric Tannier 4, 7 David P. Parsons 7
1 MORPHEO - Capture and Analysis of Shapes in Motion
Inria Grenoble - Rhône-Alpes, LJK - Laboratoire Jean Kuntzmann, Grenoble INP - Institut polytechnique de Grenoble - Grenoble Institute of Technology
7 BEAGLE - Artificial Evolution and Computational Biology
LIRIS - Laboratoire d'InfoRmatique en Image et Systèmes d'information, Inria Grenoble - Rhône-Alpes, LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
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
Treerecs is open-source. Its source code (C ++, AGPLv3) and manuals are available from https://project.inria.fr/treerecs/
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Journal articles
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https://hal.inria.fr/hal-02883386
Contributor : Celine Scornavacca Connect in order to contact the contributor
Submitted on : Tuesday, December 15, 2020 - 3:16:28 PM
Last modification on : Wednesday, November 17, 2021 - 12:31:39 PM
Long-term archiving on: : Tuesday, March 16, 2021 - 7:52:16 PM

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Nicolas Comte, Benoît Morel, Damir Hasic, Laurent Guéguen, Bastien Boussau, et al.. Treerecs: an integrated phylogenetic tool, from sequences to reconciliations.. Bioinformatics, Oxford University Press (OUP), 2020, 36 (18), pp.4822-4824. ⟨10.1093/bioinformatics/btaa615⟩. ⟨hal-02883386⟩

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