alignment=1
msa_algo_count=10
msa_args_1=-align -infile=%f.pir -outfile=%f.out -outorder=input -output=fasta
msa_args_10=%f.pir > %f.out
msa_args_2=-in %f.pir -out %f.out -stable
msa_args_3=%f.pir -output=fasta_aln -outorder=input -outfile=%f.out
msa_args_4=--auto %f.pir > %f.out
msa_name_1=clustalw
msa_name_10=nwnsi
msa_name_2=muscle
msa_name_3=t_coffee
msa_name_4=mafft
msa_opt_args_3=-special_mode=mcoffee