Temporal Multiple Statistical Alignment

A series of algorithms in evolutionary biology both involves time (temporal) and sequence (spatial) and will have different formulations depending on whether scanning is done along the temporal or the spatial dimension. Four examples already described in the literature are i. Likelihood calculations on a pedigree, where Elston and Stewart (1971) is temporal and Lander and Green (1987) is spatial. ii. Simulations under the coalescent with recombination, where Hudson (1983) is temporal and Wiuf and Hein (1999) is spatial. iii. Finding minimal recombination histories, where Song and Hein (2005) is spatial and Lyngsų, Song and Hein (2006) is temporal. iv. Score based multiple alignment was originally formulated spatially (Sankoff, 1975), but in a generalisation including affine gap penalty Knudsen (2003) switched to a temporal formulation. Multiple Statistical Alignment Algorithm is traditionally spatial (Hein, Jensen and Pedersen, 2003), but here we propose developoing a temporal version.