##' @rdname get.tree-methods
 ##' @exportMethod get.tree
 setMethod("get.tree", signature(object="apeBootstrap"),
           function(object,...) {
               object@phylo
           }
           )
 
 ##' get.tree method
 ##'
 ##'
 ##' @docType methods
 ##' @name get.tree
 ##' @rdname get.tree-methods
 ##' @aliases get.tree,beast
 ##' @exportMethod get.tree
 ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
 ##' @usage get.tree(object, ...)
 setMethod("get.tree", signature(object="beast"),
           function(object,...) {
               object@phylo
           }
           )
 
 
 ##' @rdname get.tree-methods
 ##' @exportMethod get.tree
 ##' @param by one of rst or mlc
 setMethod("get.tree", signature(object="codeml"),
           function(object, by="rst", ...) {
               if (by == "rst") {
                   return(object@rst@phylo)
               } else {
                   return(object@mlc@phylo)
               }
           })
 
 
 ##' @rdname get.tree-methods
 ##' @exportMethod get.tree
 setMethod("get.tree", signature(object="jplace"),
           function(object) {
               object@phylo
           })
 
 ##' @rdname get.tree-methods
 ##' @exportMethod get.tree
 setMethod("get.tree", signature(object = "nhx"),
           function(object) {
               object@phylo
           }
           )
 
 ##' @rdname get.tree-methods
 ##' @exportMethod get.tree
 setMethod("get.tree", signature(object="phylip"),
           function(object,...) {
               object@phylo
           }
           )
 

 ##' @rdname get.tree-methods
 ##' @exportMethod get.tree
 setMethod("get.tree", signature(object="phylo"),
           function(object, ...) {
               return(object)
           })