I would like to calculate QVI (quantitative convergence index) for a set of continuous characters with ancestral states reconstructed under squared parsimony assumption. In order to do it I need to calculate the maximum and minimum amount of changes over (any) phylogeny possible but I could not have found any equation.
Thank You in advance!
perhaps this may help you.
https://phylo.bio.ku.edu/slides/BIOL848-lec9-Distances.pdf
It would be worth checking out the 'ape' and 'phangorn' packages in R. While I haven't carried out the exact procedure you are describing, I have used these packages to calculate tree lengths under the parsimony criterion.
You might check Mesquite [http://mesquiteproject.wikispaces.com/].
Thank You for Your answers! Unfortunately I have already checked aforementioned R packages and, as far as I know, they can only perform such analyses under linear parsimony. With mesquite there is also some sort of issue - it requires hard polytomy assumption prior to calculation but even after change in settings it doesn't perform well (i do not know why).
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