% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/phangorn.R
 \name{phyPML}
 \alias{phyPML}
 \title{treeAnno.pml}
 \usage{
 phyPML(pmlTree, type = "ml")
 }
 \arguments{
 \item{pmlTree}{tree in pml object, output of phangorn::optim.pml}
 
 \item{type}{one of 'ml' and 'bayes' for inferring ancestral sequences}
 }
 \value{
 phangorn object
 }
 \description{
 tree annotation of sequence substitution by comparing to parent node
 }
 \author{
 Yu Guangchuang
 }