updates to r script and single marker mafft/muscle fixes, fixes #31

Author: Elizabeth McDaniel

bin/groups.txt

@@ -260,7 +260,7 @@ fastas = glob.glob(prots)
 for fasta in fastas:
     outname = os.path.basename(fasta).replace(".faa", "").strip().splitlines()[0]
     output= OUTPUT + "/results/"+outname+".aln"
-    musc_cmd = ["muscle","-quiet","-in",fasta,"-out",output]
+    musc_cmd = ["mafft","-quiet",fasta,">",output]
     subprocess.call(musc_cmd)
 
 # Make tree