Maximum agreement subtree

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.

Value

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

Details

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

References

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

See also

SPR.dist

Author

Klaus Schliep klaus.schliep@gmail.com based on code of Gabriel Valiente

Examples

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