Hello Guy,
Thanks for pointing out this issue.
This sounds like a relatively trivial matter to fix.  I have added a 
sourceforge bug report which can be used to track progress on solving 
the issue:
http://sourceforge.net/tracker/index.php?func=detail&aid=1942680&group_id=181544&atid=897627

-Aaron

Guy Plunkett III wrote:
> Working in a mixed-platform environment, I periodically run into eol 
> (end-of-line) issues causing problems with software. I've been bitten by this 
> several times recently with Mauve: the Mac version will work on files with 
> Unix end-of-lines (LF) but not those with Mac end-of-lines (CR); I'm not sure 
> about Windows files (CRLF). This is fine, except there is no error message or 
> indication of a problem with the fasta file -- Mauve just does nothing. Is 
> there some way to either (a) make Mauve eol-agnostic, or (b) generate an 
> error message if there is a problem with an input file?
>
> Thanks,
> Guy
>   


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