-> MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_muscle $_muscle_05_%[RSL]%.aln
-> PHYLO_PL %[PHYLO_OPT]% $_muscle_05_%[RSL]%.aln $_muscle_05_%[RSL]% %[TMP_DIR]%
+> MSA_PRO -o=p -n=10 -d -rr=0.5 -c -rsl=%[RSL]% $_muscle $_muscle_05_%[RSL]%.aln
+> PHYLO_PL %[PHYLO_OPT]% $_muscle_05_%[RSL]%.aln $_muscle_05_%[RSL]% %[TMP_DIR]%
+-
+
+> MUSCLE -maxiters 1000 -maxtrees 100 -in $ -out $_muscle_
+> MSA_PRO -o=p -n=10 -d -rr=0.9 -c -rsl=%[RSL]% $_muscle_ $_muscle_09_%[RSL]%.aln
+> PHYLO_PL %[PHYLO_OPT]% $_muscle_09_%[RSL]%.aln $_muscle_09_%[RSL]% %[TMP_DIR]%