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.TH "alignment-draw" "1" "Feb 2018" "" ""
.hy
.SH NAME
.PP
\f[B]alignment-draw\f[R] - Draw an alignment to HTML, optionally
coloring residues by AU.
.SH SYNOPSIS
.PP
\f[B]alignment-draw\f[R] \f[I]alignment\f[R] [\f[I]AU file\f[R]]
[OPTIONS]
.SH DESCRIPTION
.PP
Draw an alignment to HTML, optionally coloring residues by AU.
.SH GENERAL OPTIONS:
.TP
\f[B]-h\f[R], \f[B]--help\f[R]
produce help message
.TP
\f[B]--file\f[R] \f[I]arg\f[R]
file with sequences and initial alignment
.TP
\f[B]--legend\f[R]
Print a legend showing how color-scheme indicates uncertainty.
.TP
\f[B]--show-ruler\f[R]
Print a ruler to show column numbers
.TP
\f[B]--column-colors\f[R]
Color-code column ticks by column certainty
.TP
\f[B]--AU\f[R] \f[I]arg\f[R]
file with alignment uncertainties
.TP
\f[B]--show-gaps\f[R] \f[I]arg\f[R] (=yes)
Show gaps
.TP
\f[B]--gaps-different\f[R] \f[I]arg\f[R] (=yes)
Color gaps in grey.
.TP
\f[B]--width\f[R] \f[I]arg\f[R]
The number of columns per line
.TP
\f[B]--start\f[R] \f[I]arg\f[R]
The first column to plot
.TP
\f[B]--end\f[R] \f[I]arg\f[R]
The last column to plot
.TP
\f[B]--format\f[R] \f[I]arg\f[R] (=HTML)
produce a plot in this format
.TP
\f[B]--min\f[R] \f[I]arg\f[R]
Minimum value of scale function
.TP
\f[B]--max\f[R] \f[I]arg\f[R]
Maximum value of scale function
.TP
\f[B]--color-scheme\f[R] \f[I]arg\f[R]
Include a length of how certainties map to colors
.TP
\f[B]--scale\f[R] \f[I]arg\f[R] (=LOD)
scale for the uncertainties
.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.