How to output colored alignment from clustal omega stand alone tool?
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4.5 years ago
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Is there any way to output colored multiple sequence alignment from Clustal Omega? We can easily do that on its website but I am unable to find any such option in its stand-alone version. Or is there any other similar tool, which can do that. Any help would be appreciated. Thanks!

Clustal Omega Colored alignment • 3.1k views
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A former intern (student) of me made a tool once, which can do that using the clustalW tool in the linux command line. The tool is called ADOMA, she used it for her pipeline that she made during her project.

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ADOMA does not work for me. It only prints out blank HTML that I can't use.

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Can you define what you mean by output? You want them to be printable?

You could take a look at this thread: Printable visualizations of large-scale alignments

alv is pretty cool. Otherwise there's my solution in this thread using LaTeX: Is there a command line tool that can take an alignment fasta and input and outputs an image?

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alv cannot save output, it can only print to a terminal, which doesn't really help very much

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I havent looked at this in some time, but I think its possible to capture the output of alv in a way you can use in an image, however there are probably better tools for this (my go to would be the LaTeX solution I mentioned)

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