compatibleSplits: Extract compatible splits

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

Extract compatible splits

Description

Given an object of class splits, first discards any with weight less than a tolerance, and then further removes all remaining splits that are incompatible with any other remaining one.

Usage

compatibleSplits(sp, tol = 0, plot = FALSE)

Arguments

sp	an object of class splits
tol	splits with weights below tol are dropped
plot	a logical; if TRUE plots tree displaying remaining spilts

Value

splits objects containing only those that are compatible and high weight

See Also

treeFromSplits, TINNIK

Examples

data(pTableYeastRokas)
dist=NANUQdist(pTableYeastRokas, alpha=.05, beta=.95,outfile=NULL)
nn=neighborNet(dist)
plot(nn,"2D")
tob=treeFromSplits(compatibleSplits(nn$splits),plot=TRUE) #produce tree of blobs of splits graph

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