Coloring Multiple Sequence Alignments




  1. t_coffee -other_pg seq_reformat -in dataset.aln -in3 dataset.aln -action +3convert A0 -output color_html > colored.html
    Note: the number '3' indicates that convert should be carried out on the file entered via -in3
  2. t_coffee -other_pg seq_reformat -in dataset.aln -action +color_residue 1qq4A 5 4 -output color_html > colored.html
  3. t_coffee -other_pg seq_reformat -in dataset.aln -action +color_residue 1qq4A 5 4 +color_residue 1qq4A 7 4 -output color_html > colored.html
  4. t_coffee -other_pg seq_reformat -in dataset.aln -action +edit_residue 1qq4A 5 x
  5. t_coffee -other_pg seq_reformat -in dataset.aln -in3 dataset.aln -action +3evaluate idmat +3convert 01234x -output color_html > x.html
  6. t_coffee -other_pg seq_reformat -in dataset.aln -in3 dataset.aln -action +3evaluate pam250mt +3convert 01234x -output color_html > x.html
  7. t_coffee -other_pg seq_reformat -in dataset.aln -in3 dataset.aln -action +3evaluate boxshade -output color_html > x.html

Questions should be sent to C.Notredame