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:
Or you can use this site as online clustal to stockholm converter by selecting your formats &
file.
Sequence Converter Home page
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)