期刊
JOURNAL OF COMPUTATIONAL BIOLOGY
卷 16, 期 10, 页码 1399-1418出版社
MARY ANN LIEBERT, INC
DOI: 10.1089/cmb.2009.0095
关键词
algorithms; combinatorics; gene duplications and losses; gene families evolution
类别
资金
- NSERC
We describe algorithms to study the space of all possible reconciliations between a gene tree and a species tree, that is counting the size of this space, uniformly generate a random reconciliation, and exploring this space in optimal time using combinatorial operators. We also extend these algorithms for optimal and sub-optimal reconciliations according to the three usual combinatorial costs (duplication, loss, and mutation). Applying these algorithms to simulated and real gene family evolutionary scenarios, we observe that the LCA (Last Common Ancestor) based reconciliation is almost always identical to the real one.
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