
superTree
allows the estimation of a rooted supertree from a set of rooted trees using Matrix representation parsimony. coalSpeciesTree
estimates species trees and can multiple individuals per species.superTree(tree, method = "optim.parsimony", rooted=TRUE, ...)
coalSpeciesTree(tree, X, sTree = NULL)
multiPhylo
phyDat
object to define which individual belongs to which species.phylo
.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.coalSpeciesTree
estimates a single linkage tree as suggested by Liu et al. (2010) from the element wise minima of the cophenetic matrices of the gene trees. It extends speciesTree
in ape as it allows that have several individuals per gene tree.
mrp.supertree
, speciesTree
, densiTree
, hclust
data(Laurasiatherian)
set.seed(1)
bs <- bootstrap.phyDat(Laurasiatherian, FUN = function(x)upgma(dist.hamming(x)), bs=50, multicore=FALSE)
class(bs) <- 'multiPhylo'
plot(superTree(bs))
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