Folks -- I believe that the distances predicted from the tree are called "patristic distance". They are a quite old concept. I don't have the literature accessible right now but believe they were first described by JS Farris or by Jim Rohlf. Searching on Google using that phrase yields more tools.
Cophenetic correlation is the correlation coefficient (the ordinary Pearson correlation) between the observed distances and the patristic distances. Farris pointed out in the early 1970s that minimizing it chooses the same tree as minimizing the unweighted least squares fit of the distances. Joe --- Joe Felsenstein, j...@gs.washington.edu Department of Genome Sciences and Department of Biology University of Washington Box 355065 Seattle WA 98195-5065 _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
