Displays aligned sequences, with colouring and boxing emboss prettyplot -sequences $input1 -graph png -goutfile $out_file1 -residuesperline $residuesperline -resbreak $resbreak -ccolours $ccolours -cidentity $cidentity -csimilarity $csimilarity -cother $cother -docolour $docolour -gtitle $title -pair $pair -identity $identity -box $box -boxcol $boxcol -boxcolval $boxcolval -name $name -maxnamelen $maxnamelen -number $number -listoptions $listoptions -consensus $consensus -collision $collision -alternative $alternative -showscore $showscore -portrait $portrait -auto Sequence The number of residues to be displayed on each line Residues before a space Colour residues by their consensus value Yes No Colour to display identical residues Colour to display similar residues Colour to display other residues Colour residues by table oily, amide etc. No Yes Display the title Yes No Values to represent identical similar related Only match those which are identical in all sequences Display prettyboxes Yes No Colour the background in the boxes No Yes Colour to be used for background Display the sequence names Yes No Margin size for the sequence name Display the residue number Yes No Display the date and options used Yes No Display the consensus No Yes Allow collisions in calculating consensus Yes No Use alternative collisions routine Normal collision check Checks identical scores with the max score found. So if any other residue matches the identical score then a collision has occurred If another residue has a greater than or equal to matching score and these do not match then a collision has occurred Checks all those not in the current consensus.If any of these give a top score for matching or identical scores then a collision has occured Print residue scores Set page to Portrait No Yes You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/prettyplot.html