R: Super Tree methods

superTree {phangorn} | R Documentation

## Super Tree methods

### Description

These function `superTree` allows the estimation of a supertree from a set of trees using either Matrix representation parsimony, Robinson-Foulds or SPR as criterion.

### Usage

    superTree(tree, method = "MRP", rooted = FALSE, trace = 0,
      start = NULL, multicore = FALSE, mc.cores = NULL, ...)

### Arguments

`tree` | an object of class `multiPhylo`
`method` | An argument defining which algorithm is used to optimize the tree. Possible are "MRP", "RF", and "SPR".
`rooted` | should the resulting supertrees be rooted.
`trace` | defines how much information is printed during optimization.
`start` | a starting tree can be supplied.
`multicore` | logical, whether models should estimated in parallel.
`mc.cores` | The number of cores to use, i.e. at most how many child processes will be run simultaneously.
`...` | further arguments passed to or from other methods.

### Details

The function `superTree` extends the function mrp.supertree from Liam Revells, with artificial adding an outgroup on the root of the trees. This allows to root the supertree afterwards. The functions is internally used in DensiTree. The implementation for the RF- and SPR-supertree are very basic so far and assume that all trees share the same set of taxa.

### Value

The function returns an object of class `phylo`.

### Author(s)

Klaus Schliep klaus.schliep@gmail.com Liam Revell

### References

Baum, B. R., (1992) Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon, 41, 3-10.

Ragan, M. A. (1992) Phylogenetic inference based on matrix representation of trees. Molecular Phylogenetics and Evolution, 1, 53-58.

### See Also

`mrp.supertree`, `densiTree`, `RF.dist`, `SPR.dist`

### Examples

    data(Laurasiatherian)
    set.seed(1)
    bs <- bootstrap.phyDat(Laurasiatherian,
                           FUN = function(x) upgma(dist.hamming(x)), bs=50)

    mrp_st <- superTree(bs)
    plot(mrp_st)
    ## Not run:
    rf_st <- superTree(bs, method = "RF")
    spr_st <- superTree(bs, method = "SPR")

    ## End(Not run)

[Package phangorn version 2.6.2 Index]