mast: Maximum agreement subtree

In phangorn: Phylogenetic Reconstruction and Analysis

Maximum agreement subtree

Description

mast computes the maximum agreement subtree (MAST).

Usage

mast(x, y, tree = TRUE, rooted = TRUE)

Arguments

x	a tree, i.e. an object of class phylo.
y	a tree, i.e. an object of class phylo.
tree	a logical, if TRUE returns a tree other wise the tip labels of the the maximum agreement subtree.
rooted	logical if TRUE treats trees as rooted otherwise unrooted.

Details

The code is derived from the code example in Valiente (2009). The version for the unrooted trees is much slower.

Value

mast returns a vector of the tip labels in the MAST.

Author(s)

Klaus Schliep [e-mail] based on code of Gabriel Valiente

References

G. Valiente (2009). Combinatorial Pattern Matching Algorithms in Computational Biology using Perl and R. Taylor & Francis/CRC Press

See Also

SPR.dist

Examples

tree1 <- rtree(100)
tree2 <- rSPR(tree1, 5)
tips <- mast(tree1, tree2)

phangorn documentation built on Sept. 17, 2024, 5:08 p.m.