How to extracts variants from multiple sequence alignment files?
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3 months ago
FadyNabil ▴ 10

I have a clustalw file in .aln format I want to get the variants only from this file

clustalw biopython fasta fastq • 382 views
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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

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Did you use Pierre's script or https://github.com/sanger-pathogens/snp-sites ?

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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

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I found that the sequences must have the same length

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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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