showalign displays an aligned set of protein or a nucleic acid sequences in a style suitable for publication.

Here is a sample session with showalign:

% showalign
Displays a multiple sequence alignment
Input sequence set: ~/align.pep
Output file [align.showalign]:

Mandatory qualifiers:

[-sequence] (seqset)

The sequence alignment to be displayed.

[-outfile] (outfile)

If you enter the name of a file, this program writes the sequence details into that file.

Optional qualifiers:

-refseq (string)

If you give the number in the alignment or the name of a sequence, it is taken as the reference sequence. The reference sequence is always shown in full and is the one against which all the other sequences are compared. If this is qualifier is set to 0, the consensus sequence is used as the reference sequence. By default, the consensus sequence is used as the reference sequence.

-[no]bottom (boolean)

If this option is true, the reference sequence is displayed at the top and bottom of the alignment.

-show (menu)

What to show.

-order (menu)

Output order of the sequences.

-[no]similarcase (boolean)

If this option is true (when -show is set to Similarities or Non-identities and a residue is similar but not identical to the reference sequence residue), the residue case is changed to lowercase. If -show is set to All, non-identical, non-similar residues are changed to lowercase. If False, no changes are made to the case of the residues on the basis of their similarity to the reference sequence.

-matrix (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.

-[no]consensus (boolean)

If this option is true, the consensus line is displayed at the bottom.

Advanced qualifiers:

-uppercase (range)

Regions to put in uppercase. If this is left blank, the sequence case is left alone. A set of regions is specified by a set of pairs of positions. The positions are integers. They are separated by any non-digit, non-alpha character. Examples of region specifications are:

24-45, 56-78
1:45, 67=99;765..888
1,5,8,10,23,45,57,99

-[no]number (boolean)

If this option is true, a line giving the positions in the alignment is displayed every 10 characters above the alignment.

-[no]ruler (boolean)

If this option is true, a ruler line marking every 5th and 10th character in the alignment is displayed.

-width (integer)

Width of sequence to display.

-margin (integer)

This sets the length of the left-hand margin for sequence names. If the margin is set at 0, no margin and no names are displayed. If the margin is set to a value less than the length of a sequence name, the sequence name is displayed truncated to the length of the margin. If the margin is set to -1, the minimum margin width that allows all the sequence names to be displayed in full (plus a space at the end of the name) is automatically selected.

-html (boolean)

Use HTML formatting.

-highlight (range)

Regions to color if formatting for HTML. If this is left blank, the sequence is left alone. A set of regions is specified by a set of pairs of positions. The positions are integers. They are followed by any valid HTML font color. Examples of region specifications are:

24-45 blue 56-78 orange
1-100 green 120-156 red

A file of ranges to color (one range per line) can be specified as @filename.

-plurality (float)

Set a cut-off for the percentage of positive scoring matches below which there is no consensus. The default plurality is taken as 50% of the total weight of all sequences in the alignment.

-setcase (float)

Sets the threshold for the scores of the positive matches above which the consensus is is uppercase, and below which the consensus is in lowercase.

-identity (float)

Provides the ability to set the required number of identities at a position for it to give a consensus. If this is set to 100%, only columns of identities contribute to the consensus.