title: Using jackknife to assess the quality of gene order phylogenies.
abstract: BACKGROUND
  In recent years, gene order data has attracted increasing attention from both biologists and computer scientists as a new type of data for phylogenetic analysis. If gene orders are viewed as one character with a large number of states, traditional bootstrap procedures cannot be applied. Researchers began to use a jackknife resampling method to assess the quality of gene order phylogenies.
  
  
  RESULTS
  In this paper, we design and conduct a set of experiments to validate the performance of this jackknife procedure and provide discussions on how to conduct it properly. Our results show that jackknife is very useful to determine the confidence level of a phylogeny obtained from gene orders and a jackknife rate of 40% should be used. However, although a branch with support value of 85% can be trusted, low support branches require careful investigation before being discarded.
  
  
  CONCLUSIONS
  Our experiments show that jackknife is indeed necessary and useful for gene order data, yet some caution should be taken when the results are interpreted.
authors.affiliation: Department of Computer Science and Engineering, University of South Carolina Columbia, SC 29028, USA.
authors.forename: Jian
authors.initials: J
authors.lastname: Shi
authors.forename: Yiwei
authors.initials: Y
authors.lastname: Zhang
authors.forename: Haiwei
authors.initials: H
authors.lastname: Luo
authors.forename: Jijun
authors.initials: J
authors.lastname: Tang
mesh_terms: D000465:Algorithms; D030541:Databases, Genetic; D019143:Evolution, Molecular; D020869:Gene Expression Profiling / Q000379:methods; D023061:Gene Order / Q000235:genetics*; D010802:Phylogeny