A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree

作者：Stadler Tanja^*; Degnan James H

来源：Algorithms for Molecular Biology, 2012, 7: 7.

DOI：10.1186/1748-7188-7-7

• Incomplete lineage sorting
• Coalescent history
• Anomalous gene tree
• Dynamic programming

Background: The ancestries of genes form gene trees which do not necessarily have the same topology as the species tree due to incomplete lineage sorting. Available algorithms determining the probability of a gene tree given a species tree require exponential computational runtime. %26lt;br%26gt;Results: In this paper, we provide a polynomial time algorithm to calculate the probability of a ranked gene tree topology for a given species tree, where a ranked tree topology is a tree topology with the internal vertices being ordered. The probability of a gene tree topology can thus be calculated in polynomial time if the number of orderings of the internal vertices is a polynomial number. However, the complexity of calculating the probability of a gene tree topology with an exponential number of rankings for a given species tree remains unknown. %26lt;br%26gt;Conclusions: Polynomial algorithms for calculating ranked gene tree probabilities may become useful in developing methodology to infer species trees based on a collection of gene trees, leading to a more accurate reconstruction of ancestral species relationships.

• 出版日期2012-4-30