I'm trying to automate clustalw workflow, but as result I need 3 output files .fasta .nexus and .dnd. I've tried many parameters but as result i get always only 2 files .fasta or .nexus and .dnd. The command I'm trying to enter into linux terminal :
clustalw -infile=third.fna -align -type=DNA -score=PERCENT \ -outfile=out.fasta -output=FASTA -outfile=out.nexus \ -output=NEXUS -maxdiv=45
Do anyone have idea how should I fix my command either it's just impossible for clustalw to ouput that amount of files at once?