nex2xml.py

#!/usr/bin/env python3

import sys
from Bio import SeqIO

for fn in sys.argv[1:]:
    with open(fn, 'r') as f:
        print('\t<data id="{}" name="alignment">'.format(fn[:-len('_unphased.nex')]))
        for record in SeqIO.parse(f, 'nexus'):
            if record.id.endswith('_1'):
                print('\t\t<sequence taxon="{}" totalcount="4" value="{}"/>'.format(record.id, record.seq))
        print('\t</data>')
    print()