FASTA of alignment region

[omac]

Hi,

This is a great tool. I have one question I hope you can help with.

Is it possible to retrieve only the sequence region where the alignment is?

If the target sequence is large then it is very difficult to find what you are looking for in the multi-line FASTA.

I can make edits to the code if necessary, but not sure where to look.

Or, alternatively, is it possible to produce a FASTA where the sequence is on one line for each ID, then at least it can be searched through without line breaks.

Thanks

[Anurag Priyam]

Thanks. In version 2.0 [1] you can download the alignment in fasta format. All three lines of the alignment are included - you would have to delete the ones you don’t want.

[1]: https://groups.google.com/g/sequenceserver/c/c98ePBzcuVE/m/lN-S35jVHgAJ

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[omac]

Thanks very much, I installed the new version and it looks great. Very fast too.