DNA partitions and morphology with polymorphism (12)

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Eric Smidt

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Jul 1, 2019, 5:47:18 AM7/1/19
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I would like to run an analysis that contains some DNA partitions and morphology with polymorphism (12), is it possible to provide a simple example with this type of coding? I stayed in doubt about the format. Do I have to load two files (DNA and Morphology) or can I just have one matrix (mixed like Mrbayes)? What about polymorphism coding, is it possible? I tried loading nexus, phy, but when the morphological partition arrives it does not recognize the characters. Sorry if it is basic, but I could not find an answer in the manual or in Cipres or in the examples of the web(iqtree.cibiv.univie.ac.at/). Best wishes Eric
Anathallis_MP_evitotal_iqtree.phy

Minh Bui

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Jul 1, 2019, 6:11:18 PM7/1/19
to IQ-TREE, Eric Smidt
Hi Eric,

IQ-TREE does not support such polymorphism, everything like "(12)” will be treated as missing data.

Otherwise, you can mix different dataypes, see: http://www.iqtree.org/doc/Complex-Models#partition-models. Note that you have to use the command line version here. The web server does not support mixed data types.

Does that answer your question?

Minh

On 1 Jul 2019, at 7:47 pm, Eric Smidt <ecs...@gmail.com> wrote:

I would like to run an analysis that contains some DNA partitions and morphology with polymorphism (12), is it possible to provide a simple example with this type of coding? I stayed in doubt about the format. Do I have to load two files (DNA and Morphology) or can I just have one matrix (mixed like Mrbayes)? What about polymorphism coding, is it possible? I tried loading nexus, phy, but when the morphological partition arrives it does not recognize the characters. Sorry if it is basic, but I could not find an answer in the manual or in Cipres or in the examples of the web(iqtree.cibiv.univie.ac.at/). Best wishes Eric

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Eric Smidt

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Jul 1, 2019, 6:23:23 PM7/1/19
to Minh Bui, IQ-TREE
Hi Minh, yes, thanks a lot.
I´m very happy with IQ-Tree
All the best.
Eric de Camargo Smidt
Prof. Associado II
Laboratório de Sistemática e Ecologia Molecular de Plantas
Departamento de Botânica, sala 446
Setor de Ciências Biológicas Centro Politécnico - UFPR
Caixa Postal 19031 Cep 81531-990
Curitiba, PR - Brasil
e-mail: ecs...@ufpr.br
http://orcid.org/0000-0002-1177-1682

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