 Imputing Phylogenetic Trees Using Tropical Polytopes over the Space of Phylogenetic TreesRuriko Yoshida ()
Mathematics, 2023, vol. 11, issue 15, 1-10 Abstract: When we apply comparative phylogenetic analyses to genome data, it poses a significant problem and challenge that some of the given species (or taxa) often have missing genes (i.e., data). In such a case, we have to impute a missing part of a gene tree from a sample of gene trees. In this short paper, we propose a novel method to infer the missing part of a phylogenetic tree using an analogue of a classical linear regression in the setting of tropical geometry. In our approach, we consider a tropical polytope, a convex hull with respect to the tropical metric closest to the data points. We show a condition that we can guarantee that an estimated tree from the method has at most a Robinson–Foulds (RF) distance of four from the ground truth, and computational experiments with simulated data and empirical data from Clavicipitaceae, which contains more than 4000 genes, show the method works well. Keywords: missing information; phylogenomics; phylogenetics; tropical geometry (search for similar items in EconPapers) Downloads: (external link) Related works: Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text Persistent link: https://EconPapers.repec.org/RePEc:gam:jmathe:v:11:y:2023:i:15:p:3419-:d:1211538 Access Statistics for this article Mathematics is currently edited by Ms. Emma He More articles in Mathematics from MDPI |
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