[Mesquitelist] hard polytomies that remain soft

[Jeike van de Poel]

>
> Dear Mesquitelist-subscribers,
>
>
> I am very sorry to bother you again, but I was wondering if this is indeed
> a bug in Mesquite; I resolved the polytomies and made sure my characters
> there were no polymorphies anymore. However, if I try to get Mesquite to
> calculate the Consistency Index for my character (which has several states,
> and whose ancestral state I want to reconstruct in a parsimonious manner,
> making use of a stepmatrix), Mesquite still tells me that 'soft
> polytomies' are not allowed, which is really weird as
> a) there are no polytomies, and
> b) I set the defaults to "Polytomies Hard by Default".
>
> Does anyone have an idea how to overcome this problem?
>
> Thank you so much for answering,
>
> Jeike van de Poel
> Student at Wageningen University
>
>
> 2012/4/12 Jeike van de Poel <jeike.vandepoel at wur.nl>
>
>> 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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