Analysis of long branch extraction and long branch shortening.
BACKGROUND
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.


RESULTS
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.


CONCLUSIONS
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.
Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK. timothydoconnor@gmail.com
Timothy
T
O'Connor
Kenneth
K
Sundberg
Hyrum
H
Carroll
Mark
M
Clement
Quinn
Q
Snell
D019295:Computational Biology / Q000379:methods*; D023281:Genomics / Q000379:methods*; D016013:Likelihood Functions; D010802:Phylogeny