title: Evaluation of methods for detecting conversion events in gene clusters.
abstract: BACKGROUND
  Gene clusters are genetically important, but their analysis poses significant computational challenges. One of the major reasons for these difficulties is gene conversion among the duplicated regions of the cluster, which can obscure their true relationships. Many computational methods for detecting gene conversion events have been released, but their performance has not been assessed for wide deployment in evolutionary history studies due to a lack of accurate evaluation methods.
  
  
  RESULTS
  We designed a new method that simulates gene cluster evolution, including large-scale events of duplication, deletion, and conversion as well as small mutations. We used this simulation data to evaluate several different programs for detecting gene conversion events.
  
  
  CONCLUSIONS
  Our evaluation identifies strengths and weaknesses of several methods for detecting gene conversion, which can contribute to more accurate analysis of gene cluster evolution.
authors.affiliation: Center for Comparative Genomics and Bioinformatics, 506 Wartik Lab, Pennsylvania State University, University Park, PA 16802, USA. gsong@bx.psu.edu
authors.forename: Giltae
authors.initials: G
authors.lastname: Song
authors.forename: Chih-Hao
authors.initials: CH
authors.lastname: Hsu
authors.forename: Cathy
authors.initials: C
authors.lastname: Riemer
authors.forename: Webb
authors.initials: W
authors.lastname: Miller
mesh_terms: D000818:Animals; D005075:Biological Evolution; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D005785:Gene Conversion; D006801:Humans; D005810:Multigene Family; D011323:Primates / Q000235:genetics; D016415:Sequence Alignment