| Autor: |
Yoshida, Ruriko, Paul, Lillian, Nesbitt, Peter |
| Předmět: |
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| Zdroj: |
Algorithms; Dec2022, Vol. 15 Issue 12, p483, 12p |
| Abstrakt: |
Unweighted Pair Group Method with Arithmetic Mean (UPGMA) is one of the most popular distance-based methods to reconstruct an equidistant phylogenetic tree from a distance matrix computed from an alignment of sequences. Since we use equidistant trees as gene trees for phylogenomic analyses under the multi-species coalescent model and since an input distance matrix computed from an alignment of each gene in a genome is estimated via the maximum likelihood estimators, it is important to conduct a robust analysis on UPGMA. Stochastic safety radius, introduced by Steel and Gascuel, provides a lower bound for the probability that a phylogenetic tree reconstruction method returns the true tree topology from a given distance matrix. In this article, we compute the stochastic safety radius of UPGMA for a phylogenetic tree with n leaves. Computational experiments show an improved gap between empirical probabilities estimated from random samples and the true tree topology from UPGMA, increasing confidence in phylogenic results. [ABSTRACT FROM AUTHOR] |
| Databáze: |
Complementary Index |
| Externí odkaz: |
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