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