ERROR: Invalid model name GTR

[joanpo...@gmail.com]

Hi,
I am using a data set where 3rd codon sites has been recoded to RY (purines and pyrimidines). Then I apply several partitions with different models. I applied a F81+G to 3rd codon sites and a GTR+G+Fo to 1st and 2nd positions. Then I got this error "ERROR: Invalid model name GTR". This is I guess because the program recognizes sequences as proteins due to the presence of RY and hence GTR model does not apply.

If I am correct, how could I solve it?

Thanks a lot for your great software.

Joan

[joanpo...@gmail.com]

I confirm that program recognize sequences as proteins

WARNING: N is not present in alignment that may cause numerical problems
WARNING: D is not present in alignment that may cause numerical problems
WARNING: Q is not present in alignment that may cause numerical problems
WARNING: E is not present in alignment that may cause numerical problems
WARNING: H is not present in alignment that may cause numerical problems
WARNING: I is not present in alignment that may cause numerical problems
WARNING: L is not present in alignment that may cause numerical problems
WARNING: K is not present in alignment that may cause numerical problems
WARNING: M is not present in alignment that may cause numerical problems
WARNING: F is not present in alignment that may cause numerical problems
WARNING: P is not present in alignment that may cause numerical problems
WARNING: S is not present in alignment that may cause numerical problems
WARNING: W is not present in alignment that may cause numerical problems
WARNING: V is not present in alignment that may cause numerical problems

[Bui Quang Minh]

Hi Joan,

please recode the 3rd codon sites into 0 and 1 (instead of R and Y). Then iqtree automatically detects it as a binary partition. And then for this binary partition please specify the model as GTR2+G instead of F81+G:

http://www.cibiv.at/software/iqtree/doc/Substitution-Models/#binary-and-morphological-models

This should resolve this problem.

Cheers, Minh

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Bui Quang Minh
Center for Integrative Bioinformatics Vienna (CIBIV)
Campus Vienna Biocenter 5, VBC5, Ebene 1
A-1030 Vienna, Austria
Phone: ++43 1 4277 74326
Email: minh.bui (AT) univie.ac.at