Pir to Nexus Sequence Converter

Input format: pir A FASTA like' format introduced by the National Biomedical Research Foundation (NBRF) for the Protein Information Resource (PIR) database, now part of UniProt.

Output format: nexus The NEXUS multiple alignment format, also known as PAUP 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.pir", "pir")
count = SeqIO.write(records, "THIS_IS_YOUR_OUTPUT_FILE.nexus", "nexus")
print("Converted %i records" % count)

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