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Save as SVG Phylogeographic map Phylogenetic tree Migration distance = f(t) Transition tree Transition chart All

Demo

Rice Yellow Mottle Virus (RYMV)

	West Africa
	East Africa
	Madagascar

West Nile Virus (WNV)

North America

Lassa Virus (LASV)

West Africa

Preferences

Geographic map orientation

Automatic

Windowing

Background color: Phylogenetic tree Migration distance = f(t) Transition tree Transition chart

Stack, on top: Geographic map Phylogenetic tree Migration distance = f(t) Transition tree Transition chart

Transitions without clustering

	Slow motion: 40
	N: Sliding Full H S
	Off
	Off
	Off

Transitions with clustering

Manual clustering

Lasso: Off	Clade: Off	Anchor: Off
Lat/Lng:	‡:	||:

Automatic clustering

K-means

k:

K-means + Lat/Lng

k:

Clusters color options

Select

color

Automatic

Set:	Bremm Cubediagonal Schumann Steiger Teuling Ziegler Hillbert

Colors from clusters

Clusters

O:

	Slow motion: 10
	N: Sliding Full H S
	Off

Path options

Layout

1

2

3

4

Opacity:	Gradient
Width:	Gradient
Offset:	Gradient

Color

Full paths

Monocolor
Gradient	root	tips

Transient paths

• ◠	◠	◠ •
Heads
Size

Highlight

◠ •

• ◠

Annotate

Layout

Background

_________Jawg Terrain Streets Light Sunny Dark _________Esri NatGeoWorld World Topo World Street _________OSM OpenTopoMap Mapnik _________CartoDB Positron Voyager Voyager Labels Under DarkMatter _________StadiaXStamen Alidade Smooth Alidade Smooth Dark Outdoors Terrain TonerLite _________CyclOSM CyclOSM

no label: _________CartoDB Positron Voyager DarkMatter _________Esri Physical Imagery ShadedRelief Ocean _________StadiaXStamen Terrain

Locations

Lat:

Lng:

Sample:

Size

O

Ancestral:

Size

O

Metadata

HPD

80%

•

◯

Velocity

sample				HPD
ancestral				HPD

HPD gradient

•

◯

Layer 1D

Gradient

Layout

Opa.:	Blur:
Rad.:	Max.:

Zoo.:

Layer 2D

Boundaries

	O:
	||:

Incidence

From:

To:

Gradient with:	Quartiles Deciles
Inf/Sup

Phylogenetic tree

Info

Layout

Ladderize: up down

δ↔:		δ↕:
||:		Font:

Scale

Time scale
Most recent sampling

Annotate

Leaf labels

Transition tree

Layout

Full	Compressed

Branch

Ladderize: up down
δ↔:	δ↕:	||:

Node

S:	O:
Sz Txt	Font:

Migration distance = f(t)

Inter-cluster exchange charts

Ancestral character states

Model:	F81	Joint
Priors:	Equiprob.	Tree freq.

Output

Display

	size
Geographic map
Phylogenetic tree
Transition tree

Threshold:	M > M - 10% M > M - 20% M > M - 30% M > M - 40% M > M - 50% M
Color scale:	Cat10 Accent Dark2 Paired Pastel1 Pastel2 Set1 Set2 Set3 Tab10 grey single hue blue single hue green single hue red single hue orange single hue YlOrBr OrRd
Opacity: