Rule align & deletions in coding regions


Quick question: Is rule_align able to fix the alignment to position deletions in coding regions in-frame with the ORFs, given the annotation file?

Thank you

@rneher Is the best one to weigh in here. He’s working hard on ‘NextAlign’ which should allow us to codon-aware alignments, which will help with some of these deletions!

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Thank you, @emmahodcroft.
Looking forward to use NextAlign. :raised_hands:t4:

@andersonbrito – you are welcome to to test it.

You can use this branch:

and get the nextalign executable as described in the README here:

but linux only atm.

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