Clustal to Stockholm Sequence Converter

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.

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, "THIS_IS_YOUR_OUTPUT_FILE.stockholm", "stockholm")
print("Converted %i records" % count)

Or you can use this site as online clustal to stockholm converter by selecting your formats & file.