Plot nucleotide diversity with multiple sequence alignment

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I have a fasta file containing sequence alignements and i woud like to plot the nucleotide divergence along the sequence positions

I have tried using DNAsp and popgenome in R but it is not really working.

The problem is that i have regions with long gaps in some sequences and i want a tool which do not calculate diversity with sequences containing gaps at a specific position but instead consider other sequences in this region without gaps ?

Can anyone suggest me a tool ?
Thanks in advance, and if I missed explaining anything, please let me know!


MSA


sequencealignement


sequencediversity

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