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:

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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 — Reply to this email directly, view it on GitHub <#1540 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AZZAVFVHYG67GCAMABRQVTDWHKQSNANCNFSM6AAAAAAR2PPHEM> . You are receiving this because you were mentioned.Message ID: ***@***.***>