Calculating the sequence similarity and percentage of matched sequences
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6.3 years ago
ago1mutant ▴ 10

I have multiple aligned fasta files containing two sequences. I would like to know the sequence similarity and percentage of matched sequences. Are there any programs or scripts that calculate the sequence similarity and percentage of matched sequences? Please let me know how to do this method.

alignment sequence • 19k views
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BLAST is the tool that does this.

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Moving to a comment since this does not answer the original question. OP has aligned fasta files for which those stats are needed.

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I hope this is the answer to your question.

https://binf.snipcademy.com/lessons/pairwise-alignment/identity-similarity

The tool you need - Blast, but read the link above before running it.

See also this post, it may be useful/

C: BLAST: Identity % and Similarity %

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@Natasha: See my comment above.

OP has a specific request. Data is already in the form of aligned fasta files. OP likely does not want to re-do alignments.

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The question is not very clear but If the aim is to find the similarity between each two sequences, BLAST can still do that. We need the OP to give more details.

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