showalign - Display a multiple sequence alignment in pretty format

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EMBOSS 6.4.0                                       05/11/2012                                      SHOWALIGN(1e)

showalign is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”).
       It is part of the "Alignment:Multiple,Data retrieval:Sequence data" command group(s).

       showalign - Display a multiple sequence alignment in pretty format

Inputsection-sequenceseqset
           The sequence alignment to be displayed.

       -matrixmatrix
           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.

   Additionalsection-refseqstring
           If you give the number in the alignment or the name of a sequence, it will be taken to be 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 set to 0 then the consensus sequence will be used as the
           reference sequence. By default the consensus sequence is used as the reference sequence.

       -bottomboolean
           If this is true then the reference sequence is displayed at the bottom of the alignment instead of
           the top. Default value: Y

       -showlist
           Default value: N

       -orderlist
           Default value: I

       -similarcaseboolean
           If this is set True, then when -show is set to 'Similarities' or 'Non-identities' and a residue is
           similar but not identical to the reference sequence residue, it will be changed to lower-case. If
           -show is set to 'All' then non-identical, non-similar residues will be changed to lower-case. If this
           is False then no change to the case of the residues is made on the basis of their similarity to the
           reference sequence. Default value: Y

       -consensusboolean
           If this is true then the consensus line is displayed. Default value: Y

   Advancedsection-uppercaserange
           Regions to put in uppercase. If this is left blank, then 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

       -numberboolean
           If this option is true then a line giving the positions in the alignment is displayed every 10
           characters above the alignment. Default value: Y

       -rulerboolean
           If this option is true then a ruler line marking every 5th and 10th character in the alignment is
           displayed. Default value: Y

       -widthinteger
           Default value: 60

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

       -htmlboolean
           Default value: N

       -highlightrange
           Regions to colour if formatting for HTML. If this is left blank, then 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 colour. Examples of region specifications are: 24-45 blue 56-78
           orange 1-100 green 120-156 red A file of ranges to colour (one range per line) can be specified as
           '@filename'.

       -pluralityfloat
           Set a cut-off for the % of positive scoring matches below which there is no consensus. The default
           plurality is taken as 50% of the total weight of all the sequences in the alignment. Default value:
           50.0

       -setcasefloat
           Sets the threshold for the scores of the positive matches above which the consensus is in upper-case
           and below which the consensus is in lower-case. By default this is set to be half of the
           (weight-adjusted) number of sequences in the alignment. Default value: @( $(sequence.totweight) / 2)

       -identityfloat
           Provides the facility of setting the required number of identities at a position for it to give a
           consensus. Therefore, if this is set to 100% only columns of identities contribute to the consensus.
           Default value: 0.0

       -gapsboolean
           If this option is true then gap characters can appear in the consensus. The alternative is 'N' for
           nucleotide, or 'X' for protein Default value: Y

   Outputsection-outfileoutfile

       showalign is fully documented via the tfm(1) system.

showalign-sequenceseqset [-matrixmatrix] [-refseqstring] [-bottomboolean] [-showlist] [-orderlist]
                 [-similarcaseboolean] [-consensusboolean] -uppercaserange-numberboolean-rulerboolean-widthinteger-margininteger-htmlboolean-highlightrange-pluralityfloat-setcasefloat-identityfloat-gapsboolean-outfileoutfileshowalign-help