Ambiguous nucleotides as input for Hyphy positive selection

[psorigue]

Hi!

I am using some methods for Hyphy positive selection. I have an alignment with 243 spp, and 2 individuals per species. For this reason, I have two different haplotypes per species. To reduce the complexity and time, I considered pooling the two haplotypes, but this will generate some ambiguous (IUPAC-symboled) nucleotides.

My question is the following: When entering a codon with a IUPAC symbol that represents two possible nucleotides, does Hyphy consider the two nucleotide options for the analyses, or does it treat the nucleotide as "missing data"? In this latter case, I would rather only choose one of the two haplotypes for the analysis.

Thanks in advance for your help.

Best, Pol Sorigué

[spond]

Dear @psorigue,

HyPhy will treat nucleotide ambiguities as partially missing data (e.g. a Y maps to [0,1,0,1] probabilities for the corresponding leaf). Partially resolved codons work the same way, e.g. CRA ~ CAA or CGA.

Hope this helps, Sergei

[psorigue]

It was indeed helpful, thank you a lot.

Missatge de Sergei Pond @.***> del dia dt., 8 de nov. 2022 a les 19:10:

Dear @psorigue https://github.com/psorigue,

HyPhy will treat nucleotide ambiguities as partially missing data (e.g. a Y maps to [0,1,0,1] probabilities for the corresponding leaf). Partially resolved codons work the same way, e.g. CRA ~ CAA or CGA.

Hope this helps, Sergei

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