Recombination as a point process along sequences

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Histories of sequences in the coalescent model with recombination can be simulated using an algorithm that takes as input a sample of extant sequences. The algorithm traces the history of the sequences going back in time, encountering recombinations and coalescence (duplications) until the ancestral material is located on one sequence for homologous positions in the present sequences. Here an alternative algorithm is formulated not as going back in time and operating on sequences, but by moving spatially along the sequences, updating the history of the sequences as recombination points are encountered. This algorithm focuses on spatial aspects of the coalescent with recombination rather than on temporal aspects as is the case of familiar algorithms. Mathematical results related to spatial aspects of the coalescent with recombination are derived.

Original languageEnglish
JournalTheoretical Population Biology
Volume55
Issue number3
Pages (from-to)248-259
Number of pages12
ISSN0040-5809
DOIs
Publication statusPublished - 1 Jan 1999
Externally publishedYes

ID: 203901394