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mast

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 klaus.schliep@gmail.com 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

Examples

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

Phylogenetic Reconstruction and Analysis

v2.7.0
GPL (>= 2)
Authors
Klaus Schliep [aut, cre] (<https://orcid.org/0000-0003-2941-0161>), Emmanuel Paradis [aut] (<https://orcid.org/0000-0003-3092-2199>), Leonardo de Oliveira Martins [aut] (<https://orcid.org/0000-0001-5247-1320>), Alastair Potts [aut], Tim W. White [aut], Cyrill Stachniss [ctb], Michelle Kendall [ctb], Keren Halabi [ctb], Richel Bilderbeek [ctb], Kristin Winchell [ctb], Liam Revell [ctb], Mike Gilchrist [ctb], Jeremy Beaulieu [ctb], Brian O'Meara [ctb], Long Qu [ctb]
Initial release

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