This article is part of the supplement: The 2009 International Conference on Bioinformatics & Computational Biology (BioComp 2009)

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Analysis of long branch extraction and long branch shortening

Timothy O’Connor1*, Kenneth Sundberg2, Hyrum Carroll2, Mark Clement2 and Quinn Snell2

Author affiliations

1 Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK

2 Department of Computer Science, Brigham Young University, Provo, Utah 84602, USA

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Citation and License

BMC Genomics 2010, 11(Suppl 2):S14  doi:10.1186/1471-2164-11-S2-S14

Published: 2 November 2010



Long branch attraction (LBA) is a problem that afflicts both the parsimony and maximum likelihood phylogenetic analysis techniques. Research has shown that parsimony is particularly vulnerable to inferring the wrong tree in Felsenstein topologies. The long branch extraction method is a procedure to detect a data set suffering from this problem so that Maximum Likelihood could be used instead of Maximum Parsimony.


The long branch extraction method has been well cited and used by many authors in their analysis but no strong validation has been performed as to its accuracy. We performed such an analysis by an extensive search of the branch length search space under two topologies of six taxa, a Felsenstein-like topology and Farris-like topology. We also examine a long branch shortening method.


The long branch extraction method seems to mask the majority of the search space rendering it ineffective as a detection method of LBA. A proposed alternative, the long branch shortening method, is also ineffective in predicting long branch attraction for all tree topologies.