used dendropy4 to assure tree and matrix have the same taxon set.

tree-covers-taxa.py

#!/usr/bin/env python
from dendropy import DnaCharacterMatrix, Tree
import sys
d = DnaCharacterMatrix.get(path=sys.argv[1],
                           schema='fasta')
# make the taxon_namespace immutable, so the tree does not add
#   new labels...
d.taxon_namespace.is_mutable = False
tree = Tree.get(path=sys.argv[2],
                schema='newick',
                preserve_underscores=True,
                taxon_namespace=d.taxon_namespace)
# get all of the taxa associated with tips of the tree, and make sure that
#   they include all of the members of the data's taxon_namespace...
treed_taxa = [i.taxon for i in tree.leaf_nodes()]
if len(treed_taxa) != len(d.taxon_namespace):
    missing = [i.label for i in d.taxon_namespace if i not in treed_taxa]
    emf = 'Some of the taxa are not in the tree. Missing "{}"\n'
    em = emf.format('", "'.join(missing))
    raise ValueError(em)