The time to the ancestor along sequences with recombination (Q1289342)

\textit{R. C. Griffiths} and \textit{P. Marjoram} [J. Compu Biol. 3, 479-502 (1996)] study the configuration of mutations in a sample of DNA sequences under an infinitely-many-sites model of mutation when recombination can occur along ancestral lineages. In this model it is assumed that point mutations which occur always segregate new sites in the sequences. The time to the most recent common ancestor (TMRCA) of a sample of sequences can vary along the sequences, since because of recombination, different parts of the sequences can have different ancestors. This paper develops a simulation algorithm for computing the expected TMRCA curve along the sequences when there is recombination, conditional on the number and positions of the segregating sites along the sequences, but not taking into account the full configuration, or the knowledge of which bases are ancestral as in Griffiths and Marjoram.