Section: New Software and Platforms

Treerecs

Keywords: Bioinformatics - Biology - Computational biology

Scientific Description: The reconciliation between gene trees and species trees is a modern method of molecular phylogeny, which does not yet have its standard software, as for example phylogeny from DNA or amino acid sequences. Treerecs has this ambition, incorporating the classic functionalities of reconciliation: annotating the vertices of a gene tree with the tops of a species tree, rooting and correcting the gene tree. Rooting and correction are calculated to minimize the number of duplications and losses in reconciliation. Medium-sized solutions are randomly sampled according to a uniform law. A likelihood can then be calculated using probabilistic methods. In addition, Treerecs is integrated into a standard software ecosystem of phylogeny, bio ++, ALE, Seaview, and has a graphical interface. Some original features are implemented, such as the possibility of combining two types of likelihoods, the one calculated from the sequences and the one calculated from the reconciliations, the possibility of estimating the costs of the evolutionary events, the possibility of exploring the space of trees according to a joined likelihood.

Functional Description: Treerecs takes as minimum input a gene tree and a species tree. It "reconciles" them, that is, it annotates gene tree nodes with events and assign them to species tree nodes. Biologically, it is a reconstruction of the gene history, given the species history, in terms of duplications, speciations, losses.

With the appropriate options Treerecs can root and correct the gene tree.

News Of The Year: Release of a 0.1 stable version

• Participants: Nicolas Comte, David P. Parsons, Eric Tannier and Benoît Morel

• Partner: Laboratoire de Biométrie et Biologie Evolutive (LBBE) - UMR CNRS 5558

• Contact: Eric Tannier