| Autor: |
David Fernández-Baca, Lei Liu |
| Jazyk: |
angličtina |
| Rok vydání: |
2019 |
| Předmět: |
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| Zdroj: |
Algorithms, Vol 12, Iss 3, p 53 (2019) |
| Druh dokumentu: |
article |
| ISSN: |
1999-4893 |
| DOI: |
10.3390/a12030053 |
| Popis: |
We study two problems in computational phylogenetics. The first is tree compatibility. The input is a collection of phylogenetic trees over different partially-overlapping sets of species. The goal is to find a single phylogenetic tree that displays all the evolutionary relationships implied by . The second problem is incomplete directed perfect phylogeny (IDPP). The input is a data matrix describing a collection of species by a set of characters, where some of the information is missing. The question is whether there exists a way to fill in the missing information so that the resulting matrix can be explained by a phylogenetic tree satisfying certain conditions. We explain the connection between tree compatibility and IDPP and show that a recent tree compatibility algorithm is effectively a generalization of an earlier IDPP algorithm. Both algorithms rely heavily on maintaining the connected components of a graph under a sequence of edge and vertex deletions, for which they use the dynamic connectivity data structure of Holm et al., known as HDT. We present a computational study of algorithms for tree compatibility and IDPP. We show experimentally that substituting HDT by a much simpler data structure—essentially, a single-level version of HDT—improves the performance of both of these algorithm in practice. We give partial empirical and theoretical justifications for this observation. |
| Databáze: |
Directory of Open Access Journals |
| Externí odkaz: |
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