DOI: 10.5061/dryad.74922
title: Data from: A Bayesian supertree model for genome-wide species tree reconstruction

description: Current phylogenomic data sets highlight the need for species tree methods
 able to deal with several sources of gene tree/species tree incongruence.
 At the same time, we need to make most use of all available data. Most
 species tree methods deal with single processes of phylogenetic
 discordance, namely, gene duplication and loss, incomplete lineage sorting
 or horizontal gene transfer. In this manuscript we address for the first
 time the problem of species tree inference from multilocus, genome-wide
 data sets in the presence of gene duplication and loss and incomplete
 lineage sorting, therefore without the need to identify orthologs or to
 use a single individual per species. We do this by extending the idea of
 Maximum Likelihood supertrees to a hierarchical Bayesian model where
 several sources of gene tree/species tree disagreement can be accounted
 for in a modular manner. We implemented this model in a computer program
 called guenomu whose input are with posterior distributions of unrooted
 gene tree topologies for multiple gene families, and whose output is the
 posterior distribution of rooted species tree topologies. We conducted
 extensive simulations under complex phylogenomic models in order to
 evaluate the performance ouf our approach in comparison with other species
 tree approaches able to deal with multilabeled trees. Our method ranked
 best, under both simulated and empirical data sets, in spite of ignoring
 branch lengths. Our results show in addition that under complex simulation
 scenarios , gene tree parsimony is also a competitive approach once we
 consider its speed in contrast to more sophisticated models.
description: Simulation
 ScriptsContains the python
 scripts used to simulate the replicate data sets, as well as the R scripts
 for recreating the manuscript and supplementary figures. This file was
 compressed with tar using the XZ format, that is, must be uncompressed
 with e.g. "tar Jxvf filename.txz" When uncompressed it will
 contain a README file with more information.Simulations_20140822.txzDrosophila gene treesData downloaded from TreeFam (http://www.treefam.org/) and processed to represent all drosophila gene families, as well as the input gene tree distributions created from them. This file was compressed with tar using the XZ format, that is, must be uncompressed with e.g. "tar Jxvf filename.txz" When uncompressed it will contain a README file with more information.drosophila.txzSupplementary FiguresSupplementary Figures mentioned in the text as SF1 to SF6, merged into one PDF file.SupplFigures_20140822.pdfguenomu software from 2013.08This file contains a link to the version of the Bayesian supertree inference software 'guenomu' used in the manuscript. The software is openly available at https://bitbucket.org/leomrtns/guenomu This file was compressed with tar using the XZ format, that is, must be uncompressed with e.g. "tar Jxvf filename.txz" When uncompressed it will contain a README file with more information.simphy software from 2013.08This file contains a link to the version of the simulation software 'SimPhy' (called "STIDSim" at the time) used in the manuscript. The software is openly available at https://code.google.com/p/simphy-project/ This file was compressed with tar using the XZ format, that is, must be uncompressed with e.g. "tar Jxvf filename.txz" When uncompressed it will contain a README file with more information.