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.