I am trying to use clustalO for Multiple Sequence Alignment on some synthetic genome files I created in fasta format but neither the web application nor the command line version accepts the input (ERROR: Cannot open input file. No alignment!).
My sequences are 5000bp in length (all the same length). The only answer I could think of was to use a dos2unix command on the file before using as input but that didn't help. Any suggestions? Is it maybe because I'm using DNA sequence (ATGC) and not protein sequence that this error occurs?