Hypothetical explanation of branch length search space Hypothetical explanation of branch length search space. I) This area is caused by the ML step predicting the β branches not being in the highest quartile, the top 25%. This is caused by α ≥ β. II) This area is created as a result of the artificial long branch created by extracting a taxa. This also masks the area important for LBA. IIIa) This area still has phylogenetic signal but is unambiguously not LBA. It is correctly identified by LBE but is not an area of interest. IIIb) The phylogenetic signal in this area has been lost to both MP and ML.
O’Connor et al. BMC Genomics 2010 11(Suppl 2):S14 doi:10.1186/1471-2164-11-S2-S14