ERROR: File not found JTTDCMut

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Caio Gueratto Coelho da Silva

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May 10, 2019, 4:11:39 PM5/10/19
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Dear Minh,

I'm trying to run an iqtree analysis of this dataset using the command line below:

iqtree -spp partition.nex -bb 1000 -alrt 1000

When the analysis start, the following error appears: 

ERROR: File not found JTTDCMut

It seem that the program is not recognizing the AA models in my dataset, because when I replace the "JTTDCMut" model by another one (e.g. TIM+F+I+G4) the error that the program shows is:

ERROR: File not found mtMAM+I+G4

Finally, when I replace all the AA models by DNA ones, the program runs the analysis normally.

Do you know how to fix this problem?
Regards,
Caio Gueratto
concatenadas_sem_varios_terminais_08_05_19.nex
partition.nex
Teste_01.phy

Minh Bui

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May 11, 2019, 4:57:21 AM5/11/19
to IQ-TREE, Caio Gueratto Coelho da Silva
Hi Caio,

Because your alignment contains DNA sequences. The Nexus file says:

FORMAT DATATYPE=DNA        FORMAT DATATYPE=DNA GAP=- MISSING=? ;

Do you have coding sequences in these partitions? Are they in frame? If yes, you can do the following:

1. Convert Nexus alignment to phylip or fasta format and use the converted file instead. This is to avoid enforcing DNA datatype.

2. Modify partition file as follows:

#nexus
begin sets;
    charset part1 = concatenadas_sem_varios_terminais_08_05_19.nex: 1-429;
    charset part2 = concatenadas_sem_varios_terminais_08_05_19.nex: 430-813;
    charset part3 = concatenadas_sem_varios_terminais_08_05_19.nex: 814-1787;
    charset part4 = concatenadas_sem_varios_terminais_08_05_19.nex: NT2AA, 1788-2429;
    charset part5 = concatenadas_sem_varios_terminais_08_05_19.nex: NT2AA, 2430-2999;
    charset part6 = concatenadas_sem_varios_terminais_08_05_19.nex: NT2AA, 3000-3308; 
    charset part7 = concatenadas_sem_varios_terminais_08_05_19.nex: 3309-3764; 
    charset part8 = Teste_01.phy:  CODON, 1-126;
charpartition mine = TIM+F+I+G4:part1,TVM+F+G4:part2,TN+F+I:part3,JTTDCMut+G4:part4,mtMAM+I+G4:part5,Dayhoff+I:part6,TIM2+F+I+G4:part7,MK+FQ+G4:part8;

end;

That means, insert NT2AA for protein partitions and CODON for codon partitions. NT2AA tells IQ-TREE to translate DNA into protein sequences using the universal genetic code. If you have other genetic code, append its ID to this keyword: http://www.iqtree.org/doc/Substitution-Models#codon-models

Hope that helps,
Minh


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<concatenadas_sem_varios_terminais_08_05_19.nex><partition.nex><Teste_01.phy>

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