The new <edit> element structure is not read properly
by Apophysis, and results in a 'List index out of bounds
(0)' error and will not load the genomes.
Sample <edit> element:
<edit date="09 Nov 2005 07:57" nick="Erik"
url="electricsheep.org" action="clone">
<edit filename="genebank.flam3" index="898"/>
</edit>
Stripping the <edit> elements with an egrep:
egrep -v 'edit' input_file > output_file
allows the genomes to be read.