MotivationA reconciliation is an annotation of the nodes of a gene tree with evolutionary events—for example, speciation, gene duplication, transfer, loss, etc.—along with a mapping onto a species tree. Many algorithms and software produce or use reconciliations but often using different reconciliation formats, regarding the type of events considered or whether the species tree is dated or not. This complicates the comparison and communication between different programs.ResultsHere, we gather a consortium of software developers in gene tree species tree reconciliation to propose and endorse a format that aims to promote an integrative—albeit flexible—specification of phylogenetic reconciliations. This format, named recPhyloXML, is accompanied by several tools such as a reconciled tree visualizer and conversion utilities.Availability and implementation http://phylariane.univ-lyon1.fr/recphyloxml/.

Phylogenetic trees illustrate the evolutionary history of genes and species. In most cases, although genes evolve along with the species they belong to, a species tree and gene tree are not identical, because of evolutionary events at the gene level like duplication or transfer. These differences are handled by phylogenetic reconciliation, which formally is a mapping between gene tree nodes and species tree nodes and branches. We investigate models of reconciliation with a gene transfer that replaces existing gene, which is a biological important event but never included in reconciliation models. Also the problem is close to a dated version of the classical subtree prune and regraft (SPR) distance problem, where a pruned subtree has to be regrafted only on a branch closer to the root. We prove that the reconciliation problem including transfer and replacement is NP-hard, and that if speciations and transfers with replacement are the only allowed evolutionary events, then it is fixed-parameter tractable (FPT) with respect to the reconciliation's weight. We prove that the results extend to the dated SPR problem.Keywords phylogenetic reconciliation · dated subtree prune and regraft SPR · gene transfer · transfer with replacement (replacing transfer) · NP hard/complete · fixed parameter tractable FPT

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/

Gene tree/species tree reconciliation is a recent decisive progress in phylogenetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by gene-scale events such as duplication, loss, transfer, which translates mathematically into a mapping between gene tree nodes and species tree nodes or branches. Gene conversion is a frequent and important biological event, which results in the replacement of a gene by a copy of another from the same species and in the same gene tree. Including this event in reconciliations has never been attempted because this changes as well the solutions as the methods to construct reconciliations. Standard algorithms based on dynamic programming become ineffective. We propose here a novel mathematical framework including gene conversion as an evolutionary event in gene tree/species tree reconciliation. We describe a randomized algorithm giving in polynomial running time a reconciliation minimizing the number of duplications, losses and conversions. We show that the space of reconciliations includes an analog of the Last Common Ancestor reconciliation, but is not limited to it. Our algorithm outputs any optimal reconciliation with non null probability. We argue that this study opens a research avenue on including gene conversion in reconciliation, which can be important for biology.

AbstractMotivationGene 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.ResultsWe 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.AvailabilityTreerecs is open-source. Its source code (C++, AGPLv3) and manuals are available from https://project.inria.fr/treerecs/Contacteric.tannier@inria.fr or david.parsons@inria.fr