Next: STEP 2 COMMANDS Up: ALSCRIPT Command Summary Previous: REQUIRED STEP 1


ADD_SEQ <int> <int>

Allows extra sequence positions to be created in an existing alignment. This permits additional annotations to be interspaced either above, below, or anywhere in the middle of an alignment. For example:

ADD_SEQ 0 10

would create an additional 10 sequences - all set to the blank character before the first sequence in the block file that has been read in.


would add an extra sequence after sequence 3.

IMPORTANT: If you use the ADD_SEQ facility to add sequences anywhere except after the last sequence, then remember that the sequence numbers will alter. All formatting commands that follow this command must use the new sequence numbering. Thus in the first example:

ADD_SEQ 0 10

what was sequence number 1 becomes sequence 11. Sequences 1-10 are the new blank sequences to be used for annotation. Note that the sequence numbers only change for commands AFTER the SETUP command, thus, multiple add_seq commands refer to the sequence number as implied by the block file.


Defines the pointsize to be used to scale the plot and space the characters. Default is 10 point.

NUMBER_SEQSIf present, then the sequence number is output with the identifier code. This is useful for finding the coordinates of residues to box or otherwise highlight.


Specifies that alignments will be plotted with the longest paper axis horizontal. (Can get longer alignments on a page this way).


Specifies that alignments will be plotted with the longest paper axis vertical (can get more sequences on a page this way).


Units are characters.

Reserves <int> characters at left of every page for plotting identifiers. Note that not all this space need be used, if a smaller pointsize is used to plot out the identifier codes, than is used for the main alignment.


Value greater than 0 that scales the default line width. The linewidth is obtained by multiplying the pointsize by this factor.



This determines the spacing between adjacent residues in the X and Y directions. The spacing is calculated as: POINTSIZE + POINTSIZE * X_SPACE_FACTORor POINTSIZE + POINTSIZE * Y_SPACE_FACTOR as appropriate. Defaults are 0.2 and 0.0 respectively.



These determine the shift relative to the residue drawing position that is given to the boxing lines. The shift is calculated as follows


The defaults are 0.3 and 0.0 respectively.

Fiddling with the X_SPACE/SHIFT values is useful to fine tune the appearance of the alignment.


Units are characters. Defines the maximum number of characters possible in the input line length. This must be greater than the maximum number of sequences (MAX_NSEQ).

e.g. MAX_INPUT_LEN 600

Increases the default value of 500 characters to 600 characters.

MAX_NSEQ <int>

Units are characters. Defines the maximum number of sequences that may be read by the program. This parameter has a large default (500). You may need to reduce it on computers with small memories.

MAX_ILEN <int>

Units are characters. The maximum length allowed for a sequence identifier code.


Defines the maximum length allowed for a sequence alignment - this may need to be reduced from the 8000 default value on smaller computers.

X_OFFSET <int> Units of points (1/72 inch).

Defines the offset along the X-axis that the alignments will be shifted prior to printing. Fiddle with this value to get a nice offset from the bottom left hand corner of the page if your page size is not A4.

Y_OFFSET <int> Units of points (1/72 inch).

As for X_OFFSET, only Y axis.

MAX_SIDE <int> Units of inches.

Defines the length of the longest side of the printer page.

MIN_SIDE <int> Units of inches.

Defines the length of the shortest side of the printer page.


Defines the vertical spacing in character units between blocks of sequences when more than one block will fit on a page - default is 0.

DEFINE_COLOUR <int> <float> <float> <float>

DEFINE_COLORDefines a colour - the first number is a number by which the colour will be referred. The following three numbers are the intensities of red, green and blue respectively. Thus:

DEFINE_COLOUR 1 0 0.2 0.8

sets colour number 1 to be a colour with no red, 0.2 green and 0.8 blue. The exact appearance of this colour will depend on the output device. If you find suitable combinations of colours for your printer, then please let me know and I shall distribute your suggestions with the program.

DO_TICKSIf present, then tick marks are drawn below the numbers at the top of the page. Otherwise no ticks are shown.


Specifies the interval for writing residue position numbers. Default is 10

NO_NUMBERSSwitches all residue numbering off.

Next: STEP 2 COMMANDS Up: ALSCRIPT Command Summary Previous: REQUIRED STEP 1