I am working on the phylogeny of a subfamily of moths and I use ace from the 
ape-package to reconstruct the ancestral state of a bunch of morphological 

I encountered a problem with the few unknown states I have on my matrix (coded 
"?", either because material for examination was missing or the state could not 
fit in any of the categories): they are treated as other characters. Is there a 
way to ignore them? Is there a way to estimate the state for the species with 
missing information? I know it is possible to estimate the state at a tip with 
missing information in functions like AncTresh (using bayesian reconstruction) 
from the phytools package, but I am not sure if ML reconstruction can do it.

Thanks in advance to those who can enlighten me!


Th�o L�ger

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