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package Bio::Phylo::Exceptions;
use Exception::Class (
...
    { isa => 'Bio::Phylo::Exceptions' }
);
1;

use Scalar::Util qw(looks_like_number);

...
   ? $self->{'NUMBER'} = $number 
   : Bio::Phylo::Exceptions::BadNumber->throw(error => 'bad number');
}

# try
eval { $obj->set_number(sdf7897) };
...
if (UNIVERSAL::isa($@,'Bio::Phylo::Exceptions::BadNumber')){
   # do something
}