Question: Can IGV visualize clustal format alignment?
0
gravatar for shadowstep
2.6 years ago by
shadowstep0
shadowstep0 wrote:

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 • 965 views
ADD COMMENTlink modified 2.6 years ago by _r_am31k • written 2.6 years ago by shadowstep0

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.

ADD REPLYlink written 2.6 years ago by guillaume.rbt830
3
gravatar for genomax
2.6 years ago by
genomax92k
United States
genomax92k wrote:

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

ADD COMMENTlink written 2.6 years ago by genomax92k
1
gravatar for Buffo
2.6 years ago by
Buffo1.8k
Buffo1.8k wrote:

You can visulize it with Jalview

ADD COMMENTlink written 2.6 years ago by Buffo1.8k
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