Provided by: bali-phy_3.6.1+dfsg-2build3_amd64
NAME
alignment-draw - Draw an alignment to HTML, optionally coloring residues by AU.
SYNOPSIS
alignment-draw alignment [AU file] [OPTIONS]
DESCRIPTION
Draw an alignment to HTML, optionally coloring residues by AU.
GENERAL OPTIONS:
-h, –help produce help message –file arg file with sequences and initial alignment –legend Print a legend showing how color-scheme indicates uncertainty. –show-ruler Print a ruler to show column numbers –column-colors Color-code column ticks by column certainty –AU arg file with alignment uncertainties –show-gaps arg (=yes) Show gaps –gaps-different arg (=yes) Color gaps in grey. –width arg The number of columns per line –start arg The first column to plot –end arg The last column to plot –format arg (=HTML) produce a plot in this format –min arg Minimum value of scale function –max arg Maximum value of scale function –color-scheme arg Include a length of how certainties map to colors –scale arg (=LOD) scale for the uncertainties
EXAMPLES:
Rainbow+contrast+fade AA+contrast+fade+fade+fade+fade
REPORTING BUGS:
BAli-Phy online help: <http://www.bali-phy.org/docs.php>. Please send bug reports to <bali-phy-users@googlegroups.com>.
AUTHORS
Benjamin Redelings. Feb 2018 alignment-draw(1)