Fasta to Nexus Sequence Converter

Input format: fasta This refers to the input FASTA file format introduced for Bill Pearson's FASTA tool, where each record starts with a '>' line. Resulting sequences have a generic alphabet by default.

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.fasta", "fasta")
count = SeqIO.write(records, "THIS_IS_YOUR_OUTPUT_FILE.nexus", "nexus")
print("Converted %i records" % count)

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