Auspice

Summary

Auspice is software that performs visualization of Phylogenetic

phylogenies.

Property	Description	Example
color_by	Colouring	"country"
geo_resolution	Geographic resolution	"country"
distance_measure	Phylogeny x-axis measure	"div" or "num_date"
map_triplicate	Should the map repeat, so that you can pan further in each direction?	Boolean
layout	Tree layout	"rect", "radial", "unrooted", "clock" or "scatter"
branch_label	Which set of branch labels are to be displayed	"aa", "lineage"
panels	List of panels which (if available) are to be displayed	["tree", "map"]
transmission_lines	Should transmission lines (if available) be rendered on the map?	Boolean
language	Language to display Auspice in	"ja"

Key	Description	Example(s)
c	Colouring to use	c=author, c=region
r	Geographic resolution	r=region
m	Phylogeny x-axis measure	m=div
l	Phylogeny layout	l=clock
scatterX	Scatterplot X variable	scatterX=num_date
scatterY	Scatterplot Y variable	scatterY=num_date
branches	Hide branches	branches=hide
regression	Show/Hide regression line	regression=hide, regression=show
transmissions	Hide transmission lines	transmissions=hide
lang	Language	lang=ja (Japanese)
dmin	Temporal range (minimum)	dmin=2008-05-13
dmax	Temporal range (maximum)	dmax=2010-05-13
f_	Data filter. Multiple values per key are , separated.	f_region=Oceania
gt	Genotype filtering
d	List of panels to display, , separated	d=tree,map
p	Panel layout (buggy!)	p=full, p=grid
gmin	Entropy panel zoom (minimum) bound	gmin=1000
gmin	Entropy panel zoom (maximum) bound	gmax=2000
animate	Animation settings
n	Narrative page number	n=1 goes to the first page
s	Selected strain	s=1_0199_PF
branchLabel	Branch labels to display	branchLabel=aa
label	Labeled branch that tree is zoomed to	label=clade:B3, label=lineage:relapse
clade	DEPRECATED Labeled clade that tree is zoomed to	clade=B3 should now become label=clade:B3
sidebar	Force the sidebar into a certain state	sidebar=closed or sidebar=open
legend	Force the legend into a certain state	legend=closed or legend=open
onlyPanels	Do not display the footer / header. Useful for iframes.	onlyPanels
ci	Display confidence intervals on the tree.	ci