I produced a multiple alignment using
mafft --clustalout seq.fasta > align.fa
Is there any tool to help visualize this alignment file? IGV user guide said that a BAM file is required, how could I produce BAM format alignment file? Thank you!
IGV is not meant to be used to visualize multiple alignment files, maybe you could use the web interface of MAFFT to do your alignement, it will produce a visual output.
Why do you need IGV to visualize a MSA? You can use JalView, MEGA, Clustal etc for this purpose.
You can visulize it with Jalview
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