I need to identify my populations from my FASTA file in R so that R can then run all my stats. However, I do not know how to tell R how to group my data into 4 populations! This is the warning message I keep getting:
Warning message:
In HsHt(g) : Need at least two population to calculate differentiation
If anyone can help I would greatly appreciate it!
You are asking a secondary question about you have problem in R and fasta analysis.
But, you should ask or define your purpose exactly what is your aim.
There might me hundreds of other ways to identify the sequence, and I would say R is not the preferred program to do that directly.
Would be easiest to just blast the sequences and group the sequences based on taxonomy.
And you mention something about population. This refers to the metadata properties and not really sequence related thing. For this you need to connect the sequence information with the metadata.
I hope this resource may be helpful for what it seems what you are trying to accomplish: https://popgen.nescent.org/PopDiffSequenceData.html
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