pass
else:
taxa_in_alignment.append(record.id)
tree = EvolTree(tree_file)
out_tree_name = os.path.basename(tree_file)
out_tree_name = os.path.splitext(out_tree_name)[0]
out_tree_name = out_tree_name + '_' + gene_name + '.tre'
# If there is a new alignment, prune the tree down to the taxa that remain in
# the new alignment and write a new tree because EvolTree is shit and can't
# use the pruned tree saved in memory
if empty_seq_count >= 1:
if len(taxa_in_alignment) >= 1:
tree.prune(taxa_in_alignment, preserve_branch_length=True)
tree.unroot()
tree.write(outfile=out_tree_name, format=0)
tree = EvolTree(out_tree_name)
tree.link_to_alignment(alignment_file)
tree.workdir = os.getcwd()
# Record list of all node_ids in the tree for later retrieving omega from a
# background branch in the b_free model
list_of_node_ids = []
for node in tree.traverse('postorder'):
list_of_node_ids.append(node.node_id)
test_taxa = []
with open(test_taxa_file, 'r') as test_taxa_list:
