Hello,
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
characters.
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!
Cheers,
Th�o L�ger
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