ape (version 1.7)

boot.phylo: Tree Bipartition and Bootstrapping Phylogenies

Description

These functions analyse bipartitions found in a series of trees.

prop.part counts the number of bipartitions found in a series of trees given as ....

prop.clades counts the number of times the bipartitions present in phy are present in a series of trees given as ... or in the list previously computed and given with part.

boot.phylo performs a bootstrap analysis.

Usage

boot.phylo(phy, x, FUN, B = 100, block = 1)
prop.part(...)
prop.clades(phy, ..., part = NULL)

Arguments

phy
an object of class "phylo".
x
a taxa (rows) by characters (columns) matrix; this may be presented as a list.
FUN
the function used to estimate phy (see details).
B
the number of bootstrap replicates.
block
the number of columns in x that will be resampled together (see details).
...
either (i) a single object of class "phylo", (ii) a series of such objects separated by commas, or (iii) a list containing such objects.
part
a list of partitions as returned by prop.part; if this is used then ... is ignored.

Value

  • prop.part returns a list with an attribute "number". The elements of this list are the observed clades, and the attribute their respective numbers.

    prop.clades and boot.phylo returns a numeric vector which ith element is the number associated to the ith node of phy.

Details

The argument FUN in boot.phylo must be the function used to estimate the tree from the original (resampled) data matrix. Thus, if the tree is estimated with neighbor-joining (see nj), one maybe wants something like FUN = function(xx) nj(dist.dna(xx)).

block in boot.phylo specifies the number of columns to be resampled altogether. For instance, if one wants to resample at the codon-level, then block = 3 must be used.

References

Efron, B., Halloran, E. and Holmes, S. (1996) Bootstrap confidence levels for phylogenetic trees. Proceedings of the National Academy of Sciences USA, 93, 13429--13434.

Felsenstein, J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783--791.

See Also

dist.topo