Full sequence data with HKY model

[nage0178]

Hello,

I am trying to simulate multiple sequence alignments with the full sequence data, not just the invariant sites with an HKY model using msprime. Is this possible? This is similar to a previous post, but it appears they are using a simpler DNA mutation model.

#1821

Thanks,
Anna Nagel

[jeromekelleher]

I think the same general advice applies, you just need to use the HKY model when simulating mutations.

[nage0178]

Thanks for your response.

To set the ancestral sequence, the previous response uses tskit.random_nucleotides. The documentation says this gives equal probability to all nucleotides. For the HKY model, the stationary distribution for the nucleotides are not equal. Is there a different way to set the ancestral sequence?

[jeromekelleher]

I see - I don't have code to generate this I'm afraid, but there should be tools out there that will generate a sequence with the required properties.