Fixed-Parameter and Approximation Algorithms for Maximum Agreement Forests

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.

36 pages, 9 figures. Removed the Approximation and TBR sections and simplified the Hybridization section. To appear in SIAM Journal on Computing

Cited by in corpus (10)

• The space of ultrametric phylogenetic trees
• Towards the fixed parameter tractability of constructing minimal phylogenetic networks from arbitrary sets of nonbinary trees
• Computing Hybridization Networks for Multiple Rooted Binary Phylogenetic Trees by Maximum Acyclic Agreement Forests
• Aggregation of Composite Solutions: strategies, models, examples
• Approximation algorithms for nonbinary agreement forests
• A practical approximation algorithm for solving massive instances of hybridization number for binary and nonbinary trees
• Computing a Relevant Set of Nonbinary Maximum Acyclic Agreement Forests
• A quadratic kernel for computing the hybridization number of multiple trees
• Algorithms for Maximum Agreement Forest of Multiple General Trees
• Fast computation of all maximum acyclic agreement forests for two rooted binary phylogenetic trees