def test_ancestor_raxml_command_verbose(self):
raxml_seq_recon = RAxMLSequenceReconstruction('input_alignment.fasta', 'input_tree',
'output_alignment_filename', 'output_tree',
'raxmlHPC -f A -p 1 -m GTRGAMMA',
verbose = True)
self.assertEqual(raxml_seq_recon.raxml_reconstruction_command(raxml_seq_recon.working_dir+'/rooted_tree.newick'), 'raxmlHPC -f A -p 1 -m GTRGAMMA -s '+raxml_seq_recon.input_alignment_filename+' -t ' + raxml_seq_recon.working_dir+'/rooted_tree.newick -n internal ')
