TreeToConstraints.R

TreeToConstraints.R

#Fasttree tree constraint in R
#http://www.microbesonline.org/fasttree/constrained.html

#Packages
library(ape)
library(phylobase)
library(adephylo)
library(bio3d)
library(pbapply)

#Use either this function of the original (listTips). listTips2 adds a progress bar.
listTips2 <- function(x){
  ## if(!require(phylobase)) stop("phylobase package is not installed")
  
  ## conversion from phylo, phylo4 and phylo4d
  x <- as(x, "phylo4")
  
  ## check phylo4 object
  if (is.character(checkval <- checkPhylo4(x))) stop(checkval)
  
  ## computations
  nodIdx <- nTips(x)+1
  nodIdx <- nodIdx:(nodIdx+nNodes(x)-1)
  res <- pblapply(nodIdx, function(i) descendants(x, i))
  
  if(hasNodeLabels(x)) {names(res) <- nodeLabels(x)}
  
  return(res)
}
 
#The target tree
x2<-rtree(20) #Simulated tree
#x2<-read.tree('yourTree.tre') #Tree file

#List the tips per node and create a matrix (rows tips, columns nodes)
listNodes<-listTips2(x2)
dat<-as.data.frame(sapply(listNodes, function(x){
  ifelse(x2$tip.label %in% names(x), 1,0)
}))
row.names(dat)<-x2$tip.label
dat<-as.matrix(dat)

#Create a fasta from the matrix
datF<-as.fasta(dat)

#Export fasta file
write.fasta(datF, file = 'cst.ft')