Treerecs: an integrated phylogenetic tool, from sequences to reconciliations

Motivation Gene and species tree reconciliation methods can be used to root gene trees 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 of 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, fast, versatile, with 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/