[Jalview-discuss] Saving sequence alignments in CLUSTAL format

Linda Kazandjian lindak84 at gmail.com
Fri Jan 8 15:52:25 GMT 2016

Dear Jalview team,

We have encountered an issue in the way how MSAs are saved using the
CLUSTAL format under specific conditions: when the length of the MSA (no
matter if DNA or protein sequences) is exactly a multiple of 60 (e.g.: 60
nucleotides, 120 nucleotides, 180…) the resulting CLUSTAL file has a
superfluous final section where only the sample ID list is reported.

This, per se, is not a problem since Jalview can re-open this file without
issues, but it gets problematic if the file has to be uploaded in the
program ClustalX. In this case ClustalX creates a 60-nt or 60-aa sequence
repetition at the end of each sample.

This problem can be avoided by first opening the CLUSTAL file with a text
editor, removing the last section of sample IDs, saving the file again and
finally opening it in ClustalX; but it already occurred to us to forget
checking this out and ending up with incorrect alignments.

I realize that this is a “cross-program” problem, but since we have always
been very impressed by your quick reaction times I was wondering if you
would be able to fix this issue from your side…unless fixing it has
negative consequences for other users, of course!

Thank you for your support,

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