[Mesquitelist] hard polytomies that remain soft

[Jeike van de Poel]

Dear Mesquitelist-subscribers,

I want to - parsimoniously- optimize discrete, polymorphic characters over
a tree, using a stepmatrix as a character model. Mesquite's website states
that Mesquite allows hard polytomies in a tree when stepmatrices are being
used.
Thus, I changed the Polytomy Assumption to 'hard', but when I try to
calculate my tree's consistency index, I still get the warning that trees
with soft polytomies are not allowed.

Log file:
Tree Window 1 showing Stored Trees > alterTree
"Set_Polytomy_Assumption_to_Hard"
Tree Window 1 showing Stored Trees > newAssistant "Values_for_Current_Tree"

(Select) #
(Mesquite) #
(Select) #
(Mesquite) # Chosen: Stored Characters

(Select data matrix) #
(Mesquite) #
(Choose character) #
(Mesquite) # Chosen: Chorismate_pathway
Parsimony Character Steps > setModelSource "Stored_Parsimony_Model"

(Choose model) #
(Mesquite) # Chosen: Step_Chorismate1
Note: (Parsimony Stepmatrix): Trees with soft polytomies not allowed in
step matrix parsimony calculations.  Calculations for one or more trees
were not completed.

(Note) #
(Mesquite) #

How can I get Mesquite to treat my polytomies as 'hard' if changing the
default assumption does not work? Or does this have anything to do with the
polymorphic character of my data?

Thank you for answering!

Sincerely,

Jeike van de Poel
MSc-student, Wageningen University
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