treeOfBlobs: Tree of blobs for a network

In MSCquartets: Analyzing Gene Tree Quartets under the Multi-Species Coalescent

Tree of blobs for a network

Description

Given extended newick, an evonet object, or an igraph object for a network, return its reduced, unrooted tree of blobs. Here 'reduced' means all nodes resulting from 2-blobs are suppressed, as are edges above the network's LSA.

Usage

treeOfBlobs(net, plot = FALSE)

Arguments

net	A network, supplied as an extended Newick string, an evonet object, or an igraph object
plot	if TRUE (default), plot the tree of blobs.

Value

An object of class phylo containing the unrooted topological tree derived from the network by contracting all blobs. All edge lengths are 1.

See Also

TINNIK

Examples

network = "(((a:1,d:1):1,(b:1)#H1:1):1,(#H1,c:1):2);"
plot(read.evonet(text=network))
treeOfBlobs(network, plot=TRUE)

MSCquartets documentation built on Oct. 31, 2024, 1:08 a.m.