You can find the input fasta file here 
http://mitlox.republika.pl/sortFasta.fasta . This file I created under
Linux and I also work with BioJava under Linux. Nothing change if I
created after the last sequence a new line.

On Fri, 26 Mar 2010 11:04:22 +0000
Richard Holland wrote:

> I can't see anything in the code that would cause that
> behaviour. :( Could you provide sample code and a supporting FASTA
> file that replicates the problem?
> 

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