Using jackknife to assess the quality of gene order phylogenies

BMC Bioinformatics

Research Article

Haiwei Luo¹  Jijun Tang²  Jian Shi²  Yiwei Zhang² 

[1] Department of Biological Sciences, University of South Carolina Columbia, 29028, SC, USA;Department of Computer Science and Engineering, University of South Carolina Columbia, 29028, SC, USA;

关键词: Gene Order;    Consensus Tree;    Internal Edge;    True Tree;    Signed Permutation;   

DOI  :  10.1186/1471-2105-11-168

 received in 2009-10-21, accepted in 2010-04-06,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundIn 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.ResultsIn 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.ConclusionsOur experiments show that jackknife is indeed necessary and useful for gene order data, yet some caution should be taken when the results are interpreted.

【 授权许可】

Unknown   
© Shi et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.