clustalw <TARGET> -outfile=<OUT> ; ClustalW
t_coffee <TARGET> -outfile <OUT> -output clustalw,html -newtree <DND> -relax_lib 0 -cache=no -n_core 1 -quiet  ; T-Coffee
mafft --clustalout <TARGET> > <OUT> ; Mafft
probalign -clustalw -nuc <TARGET> > <OUT> ; Probalign
probconsRNA -clustalw <TARGET> > <OUT> ; ProbConsRNA
mafft-qinsi --clustalout <TARGET> > <OUT> ; Mafft-qinsi
mxscarna  -clustalw <TARGET> > <OUT>  2> /dev/null ; MXSCARNA
t_coffee -in <TARGET> -mode rcoffee -outfile <OUT> -output clustalw,html -newtree <DND> -cache=no  -n_core 1 -quiet; R-Coffee
t_coffee -in <TARGET> -extend_mode rna2 -template_file=TEMPLATEFILE -template_file RCOFFEE -transform dna2rna -check_type -relax_lib 0 -outfile <OUT> -output clustalw,html -newtree <DND> -cache=no -n_core 1 -quiet ;R-Coffee-Real
t_coffee -in <TARGET> -method best_pair4rna -template_file=TEMPLATEFILE_BESTPAIR,RNA -extend_mode rna2 -outfile <OUT> -output clustalw,html -newtree <DND> -relax_lib 0 -cache=no -n_core 1 -quiet ; Best-Pair
t_coffee -in <TARGET> -mode rcoffee_consan -outfile <OUT> -output clustalw,html -newtree <DND> -cache=no -n_core 1 -quiet; Consan-Coffee
t_coffee -in <TARGET> -method sara_pair -template_file=TEMPLATEFILE,RNA -extend_mode rna2 -outfile <OUT> -relax_lib 0 -output clustalw,html -newtree <DND>  -transform dna2rna -cache=no -n_core 1 -quiet; SARA-Coffee