phangorn: superTree – R documentation

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superTree

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.

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)

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