--- a/gene_family_aligner.py	Fri Apr 07 13:13:38 2017 -0400
+++ b/gene_family_aligner.py	Fri Apr 07 13:19:26 2017 -0400
@@ -36,8 +36,8 @@
     if args.pasta_iter_limit is not None:
         cmd += ' --pasta_iter_limit %d' % args.pasta_iter_limit
 cmd += ' --num_threads %d' % args.num_threads
-if args.orthogroup_fna is not None:
-    cmd += ' --orthogroup_fna'
+if args.codon_alignments is not None:
+    cmd += ' --codon_alignments'
 if args.automated_trimming is not None:
     cmd += ' --automated_trimming'
 if args.gap_trimming is not None: