You can specify the path as follows
shell(paste('"C:/Program Files (x86)/Graphviz2.36/dot"','-Tsvg -O hh.lcp.dot'))
However, if you want to plot a tree from dissimilarities between sequences, you are probably better to use the newer simplified seqtreedisplay
function that generates the plot directly from the seqtree
object, i.e., the outcome of the seqtree
function. Normally, seqtreedisplay
should find Graphviz by itself.
For more details, look at the help page by typing help(seqtreedisplay)
.