Does the presence of degenerate nucleotides in consensus sequences affect the results of population genetic analysis?

01 March 2024 1 597 Report

I want to run STRUCTURE on a nuclear gene of an insect species. The sequences that I have received are showing the presence of degenerate nucleotides in the consensus sequences. Do I need to edit the degenerate nucleotides for STRUCTURE to run properly? I am confused since I might be removing the heterozygosity signal if I edit the degenerate nucleotides.

I want to know whether STRUCTURE will run with degenerate nucleotides present in the sequences.

Hari Shankar Gadri

Hii Arjun

this article is helpful.

Patterns of change in nucleotide diversity over gene length

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