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

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. Results In this pa...

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Vydané v:Algorithms for molecular biology Ročník 7; číslo 1; s. 7
Hlavní autori: Stadler, Tanja, Degnan, James H
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: London BioMed Central 30.04.2012
BioMed Central Ltd
Springer Nature B.V
Predmet:
Algorithms
Bioinformatics
Biomedical and Life Sciences
Cellular and Medical Topics
Colleges & universities
Computational Biology/Bioinformatics
Dynamic programming
Evolution
Gene loci
Genealogy
Genes
Life Sciences
Methods
new challenges
Phylogenetics: New data
Physiological
Probability
Topology
Trees
Coalescent history
Anomalous gene tree
Dynamic programming
Incomplete lineage sorting
ISSN:1748-7188, 1748-7188
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Shrnutí: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. 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. 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.
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ISSN:1748-7188
1748-7188
DOI:10.1186/1748-7188-7-7