Nothing
simulate.sequences <-
function(phylo.tree,
ancestral.sequence,
rate.mat=matrix(c(
c(0,1,1,1),
c(1,0,1,1),
c(1,1,0,1),
c(1,1,1,0)),4,4,
dimnames=list(
c("a","g","t","c"),
c("a","g","t","c")))){
num.nodes <- network.size(phylo.tree)
root.id <- which(is.na(as.numeric(phylo.tree$iel)))
sequence.list <<- list()
sequence.list[[root.id]] <<- ancestral.sequence
generated <- vector(mode="logical", length=num.nodes)
generated[root.id] <- TRUE
flag <- 0
sequence.bot(root.id, phylo.tree, generated, rate.mat, flag)
sequence.list
}
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