# Why does pratchet() in phangorn not find the most parsimonious trees?

I called pratchet() on a dataset with binary values for the characters and it returned a parsimony value of 35. I then calculated the parsimony value for the dataset with a tree that I myself constructed and it was 7. How is this possible at all? I thought that pratchet() was supposed to return the most parsimonious tree on the basis of the data set, but that clearly did not happen in this case. Is there other software that is guaranteed to find the most parsimonious tree?

• Please provide a minimal working example of code you have tried. That way a concrete and useful answer can be provided. – Nathan S. Watson-Haigh Jun 20 '18 at 1:12

• Thank you, I tried these. When I set the start tree to the tree that I created manually, I got the following result: Error in edgeMatrix[, k + 1] <- c(p1, e12, e34, p2, 1L) : number of items to replace is not a multiple of replacement length What does this mean? – Namenlos Jun 19 '18 at 22:03