prettyplot reads in a set of aligned DNA or protein sequences. It then displays them as graphics and highlights conserved regions in various ways.

Here is a sample session with prettyplot:

% prettyplot -resbreak=10 -boxcol -consensus -plurality=3
Displays aligned sequences, with coloring and boxing
Input sequence set: globin.msf
Graph type [x11]:
   
$ prettyplot globin.msf -plurality=3 -docolour
Displays aligned sequences, with coloring and boxing
Graph type [x11]:

Mandatory qualifiers (bold if not always prompted):

[-msf] (seqset)

File containing a sequence alignment.

-graph (graph)

Graph type.

Optional qualifiers:

-residuesperline (integer)

Number of residues to display on each line.

-resbreak (integer)

Residues before a space.

-[no]ccolours (boolean)

Color residues according to their consensus value.

-cidentity (string)

Color in which to display identical residues (default is RED).

-csimilarity (string)

Color in which to display similar residues (default is GREEN).

-cother (string)

Color in which to display other residues (BLACK).

-docolour (boolean)

Color residues by table: oily, amide etc.

-[no]title (boolean)

Do not display the title.

-shade (string)

Set to BPLW for normal shading. Setting pair equal to 1.5,1.0,0.5 is equivalent to setting shade to BPLW.

Residue score Color:

1.5 or over�BLACK (B)

1.0 to 1.5�BROWN (P)

0.5 to 1.0�WHEAT (L)

Under 0.5�WHITE (W)

The only four letters allowed are B,P,L, and W (in any order).

-pair (string)

Values representing identical, similar, or related.

-identity (integer)

Only match those which are identical in all sequences.

-[no]box (boolean)

Display prettyboxes.

-boxcol (boolean)

Color the background of the boxes.

-boxcolval (string)

Color to use for background (default is GREY).

-[no]name (boolean)

Display the sequence names.

-maxnamelen (integer)

Margin size for the sequence name.

-[no]number (boolean)

Display the residue number.

-[no]listoptions (boolean)

Display the date and options used.

-plurality (float)

Plurality check value (total weight divided by 2).

-consensus (boolean)

Display the consensus.

-[no]collision (boolean)

Allow collisions in calculating consensus.

-alternative (integer)

Use alternative collisions routine:

0. Normal collision check. (default)

1. Checks identical scores with the max score found. If any other residue matches the identical score, a collision has occurred.

2. If another residue has a greater than or equal to matching score and these do not match, a collision has occurred.

3. Checks all those not in the current consensus. If any of these gives a top score for matching or identical scores, a collision has occurred.

-matrixfile (matrix)

This is the scoring matrix file used when comparing sequences. By default, it is the file EBLOSUM62 (for proteins) or the file EDNAFULL (for nucleic sequences). These files are found in the data directory of the EMBOSS installation.

-showscore (integer)

Print residue scores.

-portrait (boolean)

Set page to portrait.

Advanced qualifiers:

-data (boolean)

Boolean value (no help text)