R: Maximum agreement subtree

mast {phangorn} | R Documentation

## 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 logicical, 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), for the original code see http://www.cs.upc.edu/~valiente/comput-biol/. 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

`SPR.dist`

### Examples

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

[Package phangorn version 2.3.1 Index]