Except for the RSWHE and BPWDRHE, the remaining methods get the same drawback in the slight level.
In contrast to methods 5 and 7, the remaining methods were much less consistent in their sensitivity to outliers across scenarios.
Most significantly, PATHd8 and Dating5 together identified five of these major clades as having crown diversification restricted to the Cenozoic (Ratites, Charadriiformes, Procellariiformes, Cuculiformes and Apodiformes), although the remaining methods generate estimates for these same nodes that are on average more than 50% older.
For generated family 1, the sensitivity of all methods (except S-method) is 1, whereas only SDPclust has a false positive rate of 0. In contrast to this, for generated family 2, only Trace Suite II and SDPclust have the sensitivity of 1, and MB-method, of 0.3, while the remaining methods fail completely (probably, due to their subfamily extraction procedures).
Furthermore, concordant SP cleavage sites were predicted by all three methods for DIA1 proteins from 6 species, with very similar cleavage sites predicted for DIA1s from a further 11 species (i.e. where 2 of the 3 methods predicted a cleavage site aligning with the concordant site, and the remaining method predicted the adjacent amino acid as the cleavage site).
The outputs from the remaining methods were easily adapted and converted to positive, negative or neutral.
Among the remaining methods, MRP_BR (10.8%) and SuperQP (11%) show the smallest mean RF distances.
Of the remaining methods, Quake ranks second two times and third five times.
Of the remaining methods, each has its own advantages and limitations.
The remaining methods were used fewer than 6 times each.
