RevBayes

`consensusTree`

Calculates the majority-rule consensus topology from a trace of trees and summarizes branch lengths.

Aliases

conTree
sumt

Usage

consensusTree(TraceTree trace, Probability cutoff, String file, Probability hpd, Bool mean, Bool sampledAncestors, Bool positiveBranchLengths)

Arguments

trace :	TraceTree (pass by reference)
	The samples of trees from the posterior.
cutoff :	Probability (pass by value)
	The minimum threshold for clade probabilities.
	Default : 0.5
file :	String (pass by value)
	The name of the file for storing the tree.
hpd :	Probability (pass by value)
	The probability mass of the highest posterior density node age interval.
	Default : 0.95
mean :	Bool (pass by value)
	Annotate node ages using the mean age instead of the median?
	Default : FALSE
sampledAncestors :	Bool (pass by value)
	Annotate sampled ancestor probs?
	Default : TRUE
positiveBranchLengths :	Bool (pass by value)
	Force negative branch lengths to be short but positive?
	Default : FALSE

Return Type

Tree

Example

# Read in tree trace
tree_trace = readTreeTrace("output/my.trees", burnin=0.25)

# Generate the majority-rule consensus tree
map_tree = consensusTree(trace=tree_trace, cutoff=0.5, file="consensus.tree")