Man page - alignment-draw(1)

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Package: bali-phy
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Manual

alignment-draw(1)

alignment-draw(1)

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
–show-letters arg (=yes): Show letters
–show-names arg (=yes): Show names
–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