diff --git a/deblur/workflow.py b/deblur/workflow.py
index 30e20d6..e6a863c 100644
--- a/deblur/workflow.py
+++ b/deblur/workflow.py
@@ -492,7 +492,7 @@ def op(x): return x in aligned_seq_ids
     return output_fp, okseqs, [blast_output_filename]
 
 
-def multiple_sequence_alignment(seqs_fp, threads=1):
+def multiple_sequence_alignment(seqs_fp, threads=1, output_fp=None):
     """Perform multiple sequence alignment on FASTA file using MAFFT.
 
     Parameters
@@ -517,7 +517,10 @@ def multiple_sequence_alignment(seqs_fp, threads=1):
     if stat(seqs_fp).st_size == 0:
         logger.warning('msa failed. file %s has no reads' % seqs_fp)
         return None
-    msa_fp = seqs_fp + '.msa'
+    if output_fp is None:
+        msa_fp = seqs_fp + '.msa'
+    else:
+        msa_fp = output_fp
     params = ['mafft', '--quiet', '--preservecase', '--parttree', '--auto',
               '--thread', str(threads), seqs_fp]
     sout, serr, res = _system_call(params, stdoutfilename=msa_fp)
diff --git a/scripts/deblur b/scripts/deblur
index dcb2c25..95a4437 100755
--- a/scripts/deblur
+++ b/scripts/deblur
@@ -325,10 +325,8 @@ def multiple_seq_alignment(seqs_fp, output_fp, threads_per_sample,
     """Multiple sequence alignment"""
     start_log(level=log_level * 10, filename=log_file)
     alignment = multiple_sequence_alignment(seqs_fp,
-                                            threads=threads_per_sample)
-
-    with open(output_fp, 'w') as f:
-        f.write(alignment.to_fasta())
+                                            threads=threads_per_sample,
+                                            output_fp=output_fp)
 
 
 # DE NOVO CHIMERA REMOVAL COMMAND