title: Phylogenetic search through partial tree mixing.
abstract: BACKGROUND
  Recent advances in sequencing technology have created large data sets upon which phylogenetic inference can be performed. Current research is limited by the prohibitive time necessary to perform tree search on a reasonable number of individuals. This research develops new phylogenetic algorithms that can operate on tens of thousands of species in a reasonable amount of time through several innovative search techniques.
  
  
  RESULTS
  When compared to popular phylogenetic search algorithms, better trees are found much more quickly for large data sets. These algorithms are incorporated in the PSODA application available at http://dna.cs.byu.edu/psoda
  
  
  CONCLUSIONS
  The use of Partial Tree Mixing in a partition based tree space allows the algorithm to quickly converge on near optimal tree regions. These regions can then be searched in a methodical way to determine the overall optimal phylogenetic solution.
authors: Department of Computer Science, Brigham Young University, Provo, UT 84602, USA.
authors: Kenneth
authors: K
authors: Sundberg
authors: Mark
authors: M
authors: Clement
authors: Quinn
authors: Q
authors: Snell
authors: Dan
authors: D
authors: Ventura
authors: Michael
authors: M
authors: Whiting
authors: Keith
authors: K
authors: Crandall
mesh_terms: D000465:Algorithms; D006801:Humans; D010802:Phylogeny; D012984:Software