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use Bio::Phylo::Parsers;
my $parser = new Bio::Phylo::Parsers;
...
# the nexus format is a mixed format, that can contain
# trees, taxa, matrices, etc.
my $arrayref = $parser->parse( -format => 'nexus', -file => $nexusfile
+ );

my $trees = $parser->parse(-format => 'nexus', -I_want => 'trees', -fi
+le => $nexusfile);