Provided by: bali-phy_3.3+dfsg-1_amd64
alignment-draw – Draw an alignment to HTML, optionally coloring residues by AU.
alignment-draw alignment [AU file] [OPTIONS]
Draw an alignment to HTML, optionally coloring residues by AU.
–help produce help message –align arg file with sequences and initial alignment –alphabet arg Set to `Codons' to prefer codon alphabets –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
BAli-Phy online help: <http://www.bali-phy.org/docs.php>. Please send bug reports to <firstname.lastname@example.org>.
Benjamin Redelings. Feb 2018 alignment-draw(1)