Work

Fixed-Parameter and Approximation Algorithms for Maximum Agreement Forests

Year: 2011

Type: preprint

Abstract: We present new and improved fixed-parameter algorithms for computing maximum agreement forests (MAFs) of pairs of rooted binary phylogenetic trees. The size of such a forest for two trees corresponds to their subtree prune-and-regraft distance and, if the agreement forest is acyclic, to their hybridization number. These distance measures are essential tools for understanding reticulate evolution. Our algorithm for computing maximum acyclic agreement forests is the first depth-bounded search algorithm for this problem. Our algorithms substantially outperform the best previous algorithms for these problems.

Source: arXiv (Cornell University)

DOI: 10.48550/arxiv.1108.2664

Authors: Whidden, Chris, Beiko, Robert G., Zeh, Norbert

Institution: Dalhousie University

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: Killam Trusts, Genome Atlantic, Natural Sciences and Engineering Research Council of Canada

OpenAlex ID: W2146804482

Cites: 33

Cited by: 27

Related to: 20