Converting from nexus to qual sequence file format
Sequence multi-format conversion tool

About nexus	The NEXUS multiple alignment format, also known as PAUP format.
About 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.
nexus content	Paste sequence here
Alphabet (optional)	None DNA RNA Protein Nucleotide

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