Coloring Multiple Sequence Alignments

  1. Use the +convert_flag and use the sequence as its own cache (see the documentation)
  2. Use +color_residue
  3. Use +color_residue two times in a row
  4. Use +edit_residue
  5. Use +evaluate and color_html as an output. The cache has to be the input #3 (-in3)
  6. Use the pam250mt rather that the idmat
  7. Use boxshade instead of pam250mt with the +evaluate flag

Questions should be sent to C.Notredame