Additional section¶
-refseq string
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.
-bottom boolean
If this is true then the reference sequence is displayed
at the bottom of the alignment instead of the top. Default value: Y
-show list
Default value: N
-order list
Default value: I
-similarcase boolean
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
-consensus boolean
If this is true then the consensus line is displayed.
Default value: Y
Advanced section¶
-uppercase range
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
-number boolean
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
-ruler boolean
If this option is true then a ruler line marking every
5th and 10th character in the alignment is displayed. Default value: Y
-width integer
Default value: 60
-margin integer
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
-html boolean
Default value: N
-highlight range
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'.
-plurality float
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
-setcase float
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)
-identity float
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
-gaps boolean
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
