Clustal to Stockholm Sequence Converter

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Convert file from: to
Alphabet: None DNA RNA Protein Nucleotide

Input format: clustal The alignment format of Clustal X and Clustal W.

Output format: stockholm The Stockholm alignment format is also known as PFAM format.

How to convert from clustal to stockholm ?

You can also convert between these formats by using command line tools.
  • On Windows install WSL, on Mac or Linux start terminal
  • Install BioPython
  • Run following script:
    from Bio import SeqIO
    records = SeqIO.parse("THIS_IS_YOUR_INPUT_FILE.clustal", "clustal")
    count = SeqIO.write(records, "", "stockholm")
    print("Converted %i records" % count)
  • Or you can use this site as online clustal to stockholm converter by selecting your formats & file.

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