I have a clustalw file in .aln format I want to get the variants only from this file
see https://github.com/sanger-pathogens/snp_sites / Getting A Vcf File From A Fasta Alignment
I try it but I got this: Alignment sequences.fasta contains sequences of unequal length. Expected length is 712 but got 688 in sequence MT364213.1
Did you use Pierre's script or https://github.com/sanger-pathogens/snp-sites ?
I used this link: https://github.com/sanger-pathogens/snp-sites
That link requires an aligned fasta format file which is not the same as .aln file you have. I suggest you use Pierre's script in this answer: Getting A Vcf File From A Fasta Alignment
aligned fasta format
I found that the sequences must have the same length
If your sequences aren't the same length, they aren't aligned, so you need to check your input data properly.
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