Partitioning by codon syntax

[Teofil Nakov]

Hi everyone,

I wonder if there is a good way to simplify the syntax for partitioning by codon when one has hundreds or thousands of alignments. Instead of looking up the length of each alignment, to use a wildcard character for the alignment length. I think the syntax below, with a `dot` as a placeholder for the length of the alignment, worked in Paup and MrBayes, but doesn't in IQTree (integer is required). Are there any tricks for doing something similar in IQTree? If not, can a feature like this be implemented.

#nexus
begin sets;
    charset part1 = 1-.\3;
    charset part1 = 2-.\3;
    charset part1 = 3-.\3;
    ...
end;

Thanks,

Teo

[Minh Bui]

Hi Teo,

This syntax is not supported in IQ-TREE (actually I was not aware of it). But it’s a reasonable request. I created a github issue as a reminder to implement it.

https://github.com/Cibiv/IQ-TREE/issues/100 

Thanks!

Minh

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