Analysis of Long Branch Extraction

Long branch attraction is a problem that afflicts phylogenetic methods and a procedure to detect a data set suffering from this problem is the long branch extraction method[1]. This method has been well cited and used by many authors for 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 found that the long branch extraction method seems to mask the majority of the search space rendering it ineffective as a detection method of LBA. One possible reason is the creation of artificial long branches by excluding taxa. We conclude that this method is not an advisable method for long branch attraction detection and other methods should be developed.

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