Markovian approximation to the finite loci coalescent with recombination along multiple sequences.
The coalescent with recombination process has initially been formulated backwards in time, but simulation algorithms and inference procedures often apply along sequences. Therefore it is of major interest to approximate the coalescent with recombination process by a Markov chain along sequences. We consider the finite loci case and two or more sequences. We formulate a natural Markovian approximation for the tree building process along the sequences, and derive simple and analytically tractable formulae for the distribution of the tree at the next locus conditioned on the tree at the present locus. We compare our Markov approximation to other sequential Markov chains and discuss various applications.
Bioinformatics Research Center, Aarhus University, Denmark. Electronic address: asger@birc.au.dk.
Asger
A
Hobolth
Department of Mathematics, Aarhus University, Denmark. Electronic address: jlj@imf.au.dk.
Jens Ledet
JL
Jensen
D000465:Algorithms; D003198:Computer Simulation; D056426:Genetic Loci; D005828:Genetics, Population / Q000379:methods*; D006801:Humans; D008390:Markov Chains; D008957:Models, Genetic; D008962:Models, Theoretical; D011156:Population Density; D011336:Probability; D011995:Recombination, Genetic
Coalescent with recombination; Conditional approach; Distance between segregating sites; Markov along sequences