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how to calculate the haplotypic, nucleotidic diversity and theta of watterson with the pegas package R

Hello,

I have 100 bacteria genoms, and I need to calculate the haplotypic, nucleotidic diversity and theta of watterson with the pegas package R

I need a help

Thank you

pegas haplotypic diversity nucleotidic diversity
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updated by h.mon h.mon • written by mimi • mimi

Hello mimi!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

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written by h.mon h.mon

As you do not provide any information on what you've tried or read so far, here is the simplest answer possible: Did you read the paper that describes the package?

Edit: Given that you've already posted a question on this, think about posting more elaborate questions, indicating what you have tried and read in order to motivate people to help you. One-liners typically do not motivate anyone.

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written by ATpoint ATpoint

Hello and thank you for your answer.

The article itself does not answer my questions, I used the pdf manual (much more detailed and clear).enter link description here

My files are genome sequences after doing an alignment.

My problem is that I divided my 100 genomes into 6 populations, and I would like to calculate the Dtajima for 6. Unfortunately I have this fault that I can not understand. enter link description here

Thank you 

setwd("C:/Users/....") 
data=list() 
for(i in 1:6) {
data[[i]]=read.fasta(paste("pop",i,sep=""))
data
names(data[[i]]) = i
require(ape)
tajima.test(data[i])
}
Warning messages:
1: In tajima.test(data[i]) : Tajima test requires at least 4 sequences
2: In tajima.test(data[i]) : Tajima test requires at least 4 sequences
3: In tajima.test(data[i]) : Tajima test requires at least 4 sequences
4: In tajima.test(data[i]) : Tajima test requires at least 4 sequences
5: In tajima.test(data[i]) : Tajima test requires at least 4 sequences
6: In tajima.test(data[i]) : Tajima test requires at least 4 sequences
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written by mimi • mimi

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