Qual to Nexus Sequence Converter

Input format: qual Qual files are a bit like FASTA files but instead of the sequence, record space separated integer sequencing values as PHRED quality scores. A matched pair of FASTA and QUAL files are often used as an alternative to a single FASTQ file.

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

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