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.Sequence Converter Home page
Or you can use this site as online clustal to stockholm converter by selecting your formats &
On Windows install WSL, on
or Linux start
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)