use Bio::Phylo::Parsers;
my $parser = new Bio::Phylo::Parsers;

# the newick format contains one or more trees.
my $trees = $parser->parse( -format => 'newick', -file => $newickfile );

# the 'taxlist' format is simply a list of names, from
# which a taxa object is created
my $taxa = $parser->parse( -format => 'taxlist', -file => $taxonfile );

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