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The mutation model is an HKY85 model with mutational bias πA+T = 0.8 and a transition/transversion ratio of 4.0.

The non-linearity in the median AUC as a function of mutation rate in the pairwise mutation model is partially explained by examining the proportion of families where performance improves versus degrades in Figure 8.

Although reversible processes are computationally convenient, a strand-symmetric (not necessarily reversible) mutation model is a more natural model to assume if the mutation process is similar on the two complementary strands of double-stranded DNA.

We further assume π(A) = π(T) and π(C) = π(G) (Chargaff second parity rule), so that the only parameter of the mutation model is the stationary AT frequency, AT = π(A) + π(T).

Although the present study cannot therefore address exactly how to tune mutation rate parameters on a per family level, it is clear from our results that out pairwise mutation model is successful in improving the detection of remote homologs of β-structural motifs.

In addition, problem-specific migration and mutation model are introduced to improve the effectiveness of the new algorithm.

Estimates of genetic distance, based on the stepwise mutation model, were large (δμ2 = 15.35; DSW = 15.35) suggesting that the MLGs do not share a close genealogical relationship [35].

An infinite allele mutation model was assumed.

Analyses using the stepwise mutation model were also carried out, but they provided similar results, so only those with the infinite allele mutation model are presented.

The Brownian motion approximation of the stepwise mutation model was applied to Y-chromosome microsatellites.

For tri-allelic single nucleotide polymorphisms, the parent-independent mutation model was used.