maxtree: Maximum Tree

Description Usage Arguments Value Author(s) References See Also Examples

Description

The function computes the Maximum Tree from multiple gene trees.

Usage

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maxtree(genetreevector,spname,taxaname,species.structure)

Arguments

genetreevector

a vector of gene trees

spname

the species names

taxaname

the names of taxa

species.structure

the correspondence between species and taxa

Value

The function returns the node matrix and tree string of the maximum tree. It also returns the species names.

Author(s)

Liang Liu lliu@uga.edu

References

Liu, L. and D.K. Pearl. Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Systematic Biology, 2007, 56:504-514.

Edwards, S.V., L. Liu., and D.K. Pearl. High resolution species trees without concatenation. PNAS, 2007, 104:5936-5941.

See Also

consense, genetree.vector

Examples

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genetreevector<-c("((((H:0.00302,C:0.00302):0.00304,G:0.00605):0.01029,O:0.01635):0.1,W:0.11635);",
"((((H:0.00402,G:0.00402):0.00304,C:0.00705):0.00929,O:0.01635):0.1,W:0.11635);");
species.structure<-matrix(0,5,5)
diag(species.structure)<-1
name<-species.name(genetreevector[1])
maxtree(genetreevector,name,name,species.structure)

bomeara/phybase documentation built on May 12, 2019, 11:35 p.m.