Hello,

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?


I've figured it out. There's no way to produce extra output file from ClustalW like [jrj.healey][1] said. More over there are two simply software's that allow us to convert .fasta file to .nexus format.

    pip install seqmagick
    seqmagick convert --output-format nexus --alphabet dna inFile.fasta outFile.nexus

also suggestion by [a.zielezinski][2] with:

    sudo apt-get install readseq
    readseq inFile.fasta -all -format=NEXUS -output=outFile.nexus

Thanks for help!
    

  [1]: https://www.biostars.org/u/20598/
  [2]: https://www.biostars.org/u/4700/