Hello, I have mainly used multiple sequence alignment, such as muscle which provides an output such as:
>seq1
ACT--GC
>seq2
ACT--GC
>seq3
etc.
I am attempting to do pairwise alignment using blastn, however rather than produce a sequence like the one above, it outputs like this:
I want to format this file such that it will appear like msa format, because I want to use a software(MEGA) that only accepts data in that form.
>query
ACT--GC
>subject
ACT--GC
I'm currently trying to use -outfmt for blastn on cmd line, but not sure which sequence of commands will generate the desired outcome. Any help is greatly appreciated. Thanks.
1 answer
Answers here should help: Converting ANY blast output file to an alignment fasta file.
Blast can not produce output in "aligned fasta" format which is what you are looking for.
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