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Hi Nicholas,
the package works under the assumption that newick formatted tree files contain multiple trees, one tree per line. It gets confused by the line feeds in your tree description. Do a search and replace on the line feeds and try again. For example, you can while(<>) through the tree, chomp off the line breaks and concatenate them all into $chomped_string, and then parse and unparse like this:
my $parser = new Bio::Phylo::Parsers;
my $tree = $parser->parse(-format => 'newick', -string => $chomped_string)->first;
my $unparser = new Bio::Phylo::Unparsers;
# NOTE: -mode => 'phylo' yields phylograms, so with branch lengths
my $svg = $unparser->unparse(-format => 'svg', -mode => 'phylo', -phylo => $tree);
W.r.t. your request for URLs: SVG allows for that, but there's currently no option to include them into graphs produced by Bio::Phylo. Good idea though, will try to implement that.
Hope this helps,
Rutger
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