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I have uploaded Bio::Phylo version 0.03. Note that this upload *should* not solve the issues you're having (but please install it anyway) - but it might?
In any case, using the following code:
use Bio::Phylo::Parsers;
use Bio::Phylo::Unparsers;
my $newick = new Bio::Phylo::Parsers;
my $trees = $newick->parse( -file => 'testfile.dnd', -format => 'Newick' );
my $svg = new Bio::Phylo::Unparsers;
my $string = $svg->unparse( -phylo => $trees->first, -format => 'Svg', -mode => 'clado' );
print $string;
And the following tree description, saved as "testfile.dnd":
(((A,B,E),C),D);
...yields what I'd except. Perhaps you could email me the tree that is giving you trouble?
Best wishes,
Rutger
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