[Bioperl-l] Bio::Tools::Run::Alignment::Muscle Problem

[Till Bayer]

Hi!

I have a script that uses the muscle module in biperl-run to align 
several groups 4 sequences. Everything seems to run fine, but after 
muscle is done I get the warning

-------------------- WARNING ---------------------
MSG: Replacing one sequence [ENSRNOG00000000187/1-4680]

---------------------------------------------------

The sequence mentioned is then missing from the alignment when I print 
it to a file, so I always end up with only 3 aligned seqences. Muscle 
correctly gets all 4 seqs to align. Is this a limitation of the 
alignment object? What can I do about it?

Till