Can IGV visualize clustal format alignment?
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4.6 years ago
shadowstep • 0

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 • 1.9k views
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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.

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4.6 years ago
GenoMax 123k

Why do you need IGV to visualize a MSA? You can use JalView, MEGA, Clustal etc for this purpose.

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4.6 years ago
Buffo ★ 2.0k

You can visulize it with Jalview

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