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.TH "alignment\-draw" "1" "Feb 2018" "" ""
.hy
.SH NAME
.PP
\f[B]alignment\-draw\f[] \- Draw an alignment to HTML, optionally
coloring residues by AU.
.SH SYNOPSIS
.PP
\f[B]alignment\-draw\f[] \f[I]alignment\f[] [\f[I]AU file\f[]] [OPTIONS]
.SH DESCRIPTION
.PP
Draw an alignment to HTML, optionally coloring residues by AU.
.SH GENERAL OPTIONS:
.TP
.B \f[B]\-\-help\f[]
produce help message
.RS
.RE
.TP
.B \f[B]\-\-align\f[] \f[I]arg\f[]
file with sequences and initial alignment
.RS
.RE
.TP
.B \f[B]\-\-alphabet\f[] \f[I]arg\f[]
Set to \[aq]Codons\[aq] to prefer codon alphabets
.RS
.RE
.TP
.B \f[B]\-\-legend\f[]
Print a legend showing how color\-scheme indicates uncertainty.
.RS
.RE
.TP
.B \f[B]\-\-show\-ruler\f[]
Print a ruler to show column numbers
.RS
.RE
.TP
.B \f[B]\-\-column\-colors\f[]
Color\-code column ticks by column certainty
.RS
.RE
.TP
.B \f[B]\-\-AU\f[] \f[I]arg\f[]
file with alignment uncertainties
.RS
.RE
.TP
.B \f[B]\-\-show\-gaps\f[] \f[I]arg\f[] (=yes)
Show gaps
.RS
.RE
.TP
.B \f[B]\-\-gaps\-different\f[] \f[I]arg\f[] (=yes)
Color gaps in grey.
.RS
.RE
.TP
.B \f[B]\-\-width\f[] \f[I]arg\f[]
The number of columns per line
.RS
.RE
.TP
.B \f[B]\-\-start\f[] \f[I]arg\f[]
The first column to plot
.RS
.RE
.TP
.B \f[B]\-\-end\f[] \f[I]arg\f[]
The last column to plot
.RS
.RE
.TP
.B \f[B]\-\-format\f[] \f[I]arg\f[] (=HTML)
produce a plot in this format
.RS
.RE
.TP
.B \f[B]\-\-min\f[] \f[I]arg\f[]
Minimum value of scale function
.RS
.RE
.TP
.B \f[B]\-\-max\f[] \f[I]arg\f[]
Maximum value of scale function
.RS
.RE
.TP
.B \f[B]\-\-color\-scheme\f[] \f[I]arg\f[]
Include a length of how certainties map to colors
.RS
.RE
.TP
.B \f[B]\-\-scale\f[] \f[I]arg\f[] (=LOD)
scale for the uncertainties
.RS
.RE
.SH EXAMPLES:
.PP
Rainbow+contrast+fade AA+contrast+fade+fade+fade+fade
.SH REPORTING BUGS:
.PP
BAli\-Phy online help: <http://www.bali-phy.org/docs.php>.
.PP
Please send bug reports to <bali-phy-users@googlegroups.com>.
.SH AUTHORS
Benjamin Redelings.