Critical I have the attached DQB1_exon4.nexus opened in an MSA view. I right click to 'Export', then 'Save subalignment', keep all original columns of the alignment but select some sequences only (e.g. all the "_local" sequences), and then I export to Fasta or to ClustalW format, and the result is the same in both cases: I have the right number of sequences, but wrong sequences: some of the sequences I had selected are not in the output, while some of the non-selected ones are in the output file.
