Dear,
the trim.seqs() command in the Windows 64bit 1.28.0 seems to output the trim.fasta and trim.names in an incorrect format. I can’t open it properly, and the next commands give an error (>XXXX is not in your name or count file, please correct). The scrap and group files are ok.
Now, I just saw that v1.29.0 was released, and this works fine 