---
name: "alignment-draw"
section: "1"
platform: "linux"
package: "bali-phy"
version: "4.0-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/alignment-draw"
---

# alignment-draw(1)

Draw an alignment to HTML, optionally coloring residues by AU.

## 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⟩\\c .

Please send bug reports to ⟨bali-phy-users@googlegroups.com⟩\\c .

## AUTHORS

Benjamin Redelings.