Wiuf C, Hein J
Institute of Biological Sciences, University of Aarhus, Aarhus, DK-8000, Denmark.
Theor Popul Biol. 1999 Jun;55(3):248-59. doi: 10.1006/tpbi.1998.1403.
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.
在具有重组的溯祖模型中,序列的历史可以使用一种以现存序列样本作为输入的算法来模拟。该算法追溯序列随时间回溯的历史,遇到重组和合并(重复),直到在当前序列的同源位置上祖先物质位于一个序列上。这里提出了一种替代算法,它不是随时间回溯并对序列进行操作,而是沿着序列在空间上移动,在遇到重组点时更新序列的历史。该算法关注的是具有重组的溯祖过程的空间方面,而不是像常见算法那样关注时间方面。推导了与具有重组的溯祖过程的空间方面相关的数学结果。