Journal
JOURNAL OF COMPUTATIONAL BIOLOGY
Volume 16, Issue 10, Pages 1399-1418Publisher
MARY ANN LIEBERT, INC
DOI: 10.1089/cmb.2009.0095
Keywords
algorithms; combinatorics; gene duplications and losses; gene families evolution
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Funding
- NSERC
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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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