title: DLRS: gene tree evolution in light of a species tree.
abstract: CONCLUSIONS
  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.
  
  
  METHODS
  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.
  
  
  BACKGROUND
  joel.sjostrand@scilifelab.se or jens.lagergren@scilifelab.se.
  
  
  BACKGROUND
  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.affiliation: Science for Life Laboratory, Stockholm University, SE-17121, Solna, Sweden. joel.sjostrand@scilifelab.se
authors.forename: Joel
authors.initials: J
authors.lastname: Sjöstrand
authors.forename: Bengt
authors.initials: B
authors.lastname: Sennblad
authors.forename: Lars
authors.initials: L
authors.lastname: Arvestad
authors.forename: Jens
authors.initials: J
authors.lastname: Lagergren
mesh_terms: D000465:Algorithms; D000818:Animals; D001499:Bayes Theorem; D019143:Evolution, Molecular; D015233:Models, Statistical; D010802:Phylogeny; D011381:Programming Languages; D016415:Sequence Alignment; D012984:Software