Man page - alignment-draw(1)

Packages contains this manual

Package:  bali-phy
apt-get install bali-phy

Manuals in package:
• alignment-consensus(1)
• cut-range(1)
• alignment-thin(1)
• alignment-max(1)
• bali-phy-pkg(1)
• bp-analyze(1)
• alignment-draw(1)
• summarize-ancestors(1)
• extract-ancestors(1)
• stats-select(1)
• mctree-mean-lengths(1)
• trees-consensus(1)
• alignment-find(1)
• bali-phy(1)
• statreport(1)
• alignment-indices(1)
• tree-mean-lengths(1)
• pickout(1)
• draw-tree(1)
• alignment-gild(1)
• alignment-distances(1)
• alignment-info(1)
• tree-tool(1)
• alignments-diff(1)
• trees-bootstrap(1)
• mcon-tool(1)
• alignment-cat(1)
• alignment-chop-internal(1)
• alignment-translate(1)
• trees-distances(1)
• bali-subsample(1)
Documentations in package:
• bali-phy

Manual

alignment-draw

NAME
SYNOPSIS
DESCRIPTION
GENERAL OPTIONS:
EXAMPLES:
REPORTING BUGS:
AUTHORS

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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.

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