FIXED-PARAMETER ALGORITHMS FOR MAXIMUM AGREEMENT FORESTS

被引：56
|
作者：
Whidden, Chris [1 ]
Beiko, Robert G. [1 ]
Zeh, Norbert [1 ]
机构：
[1] Dalhousie Univ, Fac Comp Sci, Halifax, NS, Canada
来源：
SIAM JOURNAL ON COMPUTING | 2013年 / 42卷 / 04期
基金：
加拿大自然科学与工程研究理事会;
关键词：
fixed-parameter tractability; phylogenetics; subtree prune-and-regraft distance; lateral gene transfer; hybridization; agreement forest; HYBRIDIZATION NUMBER; PHYLOGENETIC TREES; COMPUTATION; EVENTS; FPT; APPROXIMATION; COMPLEXITY; DISTANCE;
D O I：
10.1137/110845045
中图分类号：
TP301 [理论、方法];
学科分类号：
081202 ;
摘要：
We present new and improved fixed-parameter algorithms for computing maximum agreement forests 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.
引用
收藏
页码：1431 / 1466
页数：36
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