2017 Fiscal Year Annual Research Report
Fast Graph Algorithms for Phylogenetics
| Project/Area Number |
26330014
|
|---|
| Research Institution | Kyoto University |
|---|
Principal Investigator |
ジャンソン ジェスパー 京都大学, 白眉センター, 特定准教授 (60536100)
|
|---|
| Project Period (FY) |
2014-04-01 – 2018-03-31
|
| Keywords | algorithm / computational complexity / phylogenetic tree / consensus tree |
|---|
| Outline of Annual Research Achievements |
We presented a fast method for computing the rooted triplet distance between two galled trees, i.e., rooted phylogenetic networks in which all underlying undirected cycles are disjoint, that can be used to measure their similarity. Our new algorithm runs in O(n lg n) time, where n is the number of leaf labels, whereas the time complexity of the previously fastest method is O(n^{2.687}). Our strategy is to transform the input so that the answer can be obtained by running an existing algorithm for the simpler case of two phylogenetic trees a constant number of times. We implemented the new algorithm, and applying it to pairs of randomly generated galled trees with up to 500,000 leaves confirmed that it is fast in practice.
|
