I have a dataset with binary morphological characters. I am wondering if it is possible to calculate the maximum likelihood of a phylogenetic tree for this dataset, but it seems that all of the substitution models are designed for molecular data. Is there a substitution model for binary state characters? If it is possible to do this, does anyone know how to do this in the R package ape?

  • Did you look through the list of programs here: evolution.gs.washington.edu/phylip/software.html#Parsimony – Peter Menzel Nov 7 at 22:17
  • What problem do you have when using it with ape? If it is on the right input format it should work well (as far as I know) – Llopis Nov 8 at 10:10
  • @Llopis I can run it in phangorn with pml() and optim.pml(), but only with the JC69 model. That is, however, no intended to be used with binary sequence data, so I fear that the results are wrong because of this. – Namenlos Nov 8 at 18:36
  • Ok, so your problem seems more of interpretation rather than not working. I don't know these functions good enough but reading the code or the paper would help to interpret the output. – Llopis Nov 8 at 19:02

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