Embl to Stockholm Sequence Converter

Input format: embl The EMBL flat file format. Uses Bio.GenBank internally.

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.embl", "embl")
count = SeqIO.write(records, "THIS_IS_YOUR_OUTPUT_FILE.stockholm", "stockholm")
print("Converted %i records" % count)

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