SUMMARY: PrIME-DLRS (or colloquially: 'Delirious') is a phylogenetic software tool to simultaneously infer and reconcile a gene tree given a species tree. It accounts for duplication and loss events, a relaxed molecular clock and is intended for the study of homologous gene families, for example in a comparative genomics setting involving multiple species. PrIME-DLRS uses a Bayesian MCMC framework, where the input is a known species tree with divergence times and a multiple sequence alignment, and the output is a posterior distribution over gene trees and model parameters. AVAILABILITY AND IMPLEMENTATION: PrIME-DLRS is available for Java SE 6+ under the New BSD License, and JAR files and source code can be downloaded from http://code.google.com/p/jprime/. There is also a slightly older C++ version available as a binary package for Ubuntu, with download instructions at http://prime.sbc.su.se. The C++ source code is available upon request. CONTACT: joel.sjostrand@scilifelab.se or jens.lagergren@scilifelab.se. SUPPLEMENTARY INFORMATION: PrIME-DLRS is based on a sound probabilistic model (Åkerborg et al., 2009) and has been thoroughly validated on synthetic and biological datasets (Supplementary Material online).
SUMMARY: PrIME-DLRS (or colloquially: 'Delirious') is a phylogenetic software tool to simultaneously infer and reconcile a gene tree given a species tree. It accounts for duplication and loss events, a relaxed molecular clock and is intended for the study of homologous gene families, for example in a comparative genomics setting involving multiple species. PrIME-DLRS uses a Bayesian MCMC framework, where the input is a known species tree with divergence times and a multiple sequence alignment, and the output is a posterior distribution over gene trees and model parameters. AVAILABILITY AND IMPLEMENTATION: PrIME-DLRS is available for Java SE 6+ under the New BSD License, and JAR files and source code can be downloaded from http://code.google.com/p/jprime/. There is also a slightly older C++ version available as a binary package for Ubuntu, with download instructions at http://prime.sbc.su.se. The C++ source code is available upon request. CONTACT: joel.sjostrand@scilifelab.se or jens.lagergren@scilifelab.se. SUPPLEMENTARY INFORMATION: PrIME-DLRS is based on a sound probabilistic model (Åkerborg et al., 2009) and has been thoroughly validated on synthetic and biological datasets (Supplementary Material online).
Authors: Sean K McKenzie; Ingrid Fetter-Pruneda; Vanessa Ruta; Daniel J C Kronauer Journal: Proc Natl Acad Sci U S A Date: 2016-11-22 Impact factor: 11.205
Authors: Ying Chang; Sishuo Wang; Satoshi Sekimoto; Andrea L Aerts; Cindy Choi; Alicia Clum; Kurt M LaButti; Erika A Lindquist; Chew Yee Ngan; Robin A Ohm; Asaf A Salamov; Igor V Grigoriev; Joseph W Spatafora; Mary L Berbee Journal: Genome Biol Evol Date: 2015-05-14 Impact factor: 3.416
Authors: Gabriel Forn-Cuní; Edimara S Reis; Sonia Dios; David Posada; John D Lambris; Antonio Figueras; Beatriz Novoa Journal: PLoS One Date: 2014-06-13 Impact factor: 3.240
Authors: Gergely J Szöllősi; Adrián Arellano Davín; Eric Tannier; Vincent Daubin; Bastien Boussau Journal: Philos Trans R Soc Lond B Biol Sci Date: 2015-09-26 Impact factor: 6.237