These functions are used by other functions in the HyPhy package and not by users
Usage
get.recon.1(phy, phy.sub, reconcile)
Arguments
phy
The species tree to be reconciled of class “phylo”
phy.sub
The gene tree(s) to be reconciled in class “phylo” or “multiPhylo”
reconcile
A description of the relationship between the gene tree and the species tree:
either NULL; a vector of positive integers of length length(phy.sub$tip.label);
or a vector of integers and NA of length max(phy.sub$edge). (See details)