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Then we constructed 100 alignments each of which contained 20 sequences of length 200.

The MCMC approach requires optimal sampling of alignments, each of which ideally represents a single genealogy, to obtain precise estimations of τ and θ.

T-Coffee calculates pairwise alignments by combining the direct alignment of the pair with indirect alignments that aligns each sequence of the pair to a third sequence.

The latest versions of 8 different multiple alignment programs (see below) were used to construct an alignment for each of the benchmark test sets.

We then used these (consensus) sequences to construct a multiple alignment of each of the domains using Mafft [ 30] (three alignments in total).

The alignment columns in the alignments of each of these 100 genes were sampled with replacement to create a set of artificial alignments with the same lengths as the original alignments.

The conceptual position of introns has been searched in the global alignment of each pair of protein sequences.

Alignment of each of the domain sequences was done separately using ClustalW2.

A pairwise structural alignment of each of three MA structures [PDB∶1hiw, PDB∶1uph, PDB∶2hmx] against each MAPK substrate structure was performed using Vorometric [30].

Computation was performed using an alignment of each of the eight haplotypes produced in ClustalX.

The second data set contained a gap-balanced alignment of each of the subsets of the same data.