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PopGenome fasta input

Hello All-

I would like to use PopGenome to analyze sequence diversity by individual and population. My sequences are currently in fasta format. I was wondering if there is a way to put individual and population identifiers on my sequences so that I can use PopGenome to get these summary statistics?

-Any advice would be greatly appreciated

r popgenome fasta sequence
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written by tiffany.kosch • tiffany.kosch

What about set.populations() function?

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written by h.mon h.mon

I have looked into using this function, but unfortunately I can't use it until I have individual assignments. At the moment I just have a list of sequences with multiple sequences per individual. E.g.

>Variant_1_{Individual 10C}
xxxxxxxxxxxxxxxxxxxxxxxxx
>Variant_2_{Individual 10C}
xxxxxxxxxxxxxxxxxxxxxxxxx
>Variant_3_{Individual 10C}
xxxxxxxxxxxxxxxxxxxxxxxxx

...and so on. Any idea how I can add identifiers to the fasta file that PopGenome (or another Pop Genetics R program) would recognize?

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updated by h.mon h.mon • written by tiffany.kosch • tiffany.kosch

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