title: PADRE: a package for analyzing and displaying reticulate evolution.
abstract: Recent advances in gene sequencing for polyploid species, coupled with standard phylogenetic tree reconstruction, leads to gene trees in which the same species can label several leaves. Such multi-labeled trees are then used to reconstruct the evolutionary history of the polyploid species in question. However, this reconstruction process requires new techniques that are not available in current phylogenetic software packages. Here, we describe the software package PADRE (Package for Analyzing and Displaying Reticulate Evolution) that implements such techniques, allowing the reconstruction of complex evolutionary histories for polyploids in the form of phylogenetic networks.
  
  
  BACKGROUND
  PADRE is an open-source Java program freely available from http://www.uea.ac.uk/cmp/research/cmpbio/PADRE.
authors.affiliation: School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK. martin.lott@uea.ac.uk
authors.forename: Martin
authors.initials: M
authors.lastname: Lott
authors.forename: Andreas
authors.initials: A
authors.lastname: Spillner
authors.forename: Katharina T
authors.initials: KT
authors.lastname: Huber
authors.forename: Vincent
authors.initials: V
authors.lastname: Moulton
mesh_terms: D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D053263:Gene Regulatory Networks; D010802:Phylogeny; D012984:Software; D014584:User-Computer Interface