library(ape)
library(splits)

Name.tr<-read.tree("*.nwk", tree.names = NULL)
##read fully-resolved and ultrametric input tree constructed with haplotype data 

test1 <- gmyc(Name.tr, method="single", interval=c(0, 10))
##execute single threshold analysis

summary(test1)  
##show summary results

plot(test1)
##plot results

test2 <- gmyc(Name.tr, method="multiple", interval= c(0, 10))
##execute multiple threshold analysis

summary(test2)
##show summary results

plot(test2)
##plot results

compare(test1,test2) 
##compare multiple vs single threshold models