Examples#

This page contains example analyses and visualizations built with baltic. Sections group examples by application, and an example may appear in more than one section.

Basic tree plotting

simple-tree
simple tree
Ebola virusbasiccolour
simple-tree
simple tree
MERS-CoVbasiccolour
simple-tree
simple tree
WuMV-6basic

Tree manipulation

exploded-tree-high-level
exploded tree high level
Ebola virusexploded tree
exploded-tree-high-level
exploded tree high level
MERS-CoVexploded tree
exploded-tree-low-level
exploded tree low level
Ebola virusexploded tree
exploded-tree-low-level
exploded tree low level
MERS-CoVexploded tree
reduced-tree-camel
reduced tree camel
MERS-CoVreduced tree
reduced-tree-human
reduced tree human
MERS-CoVreduced tree
state-collapsed-tree
state collapsed tree
traitsEbola virusstate-collapsed
state-collapsed-tree
state collapsed tree
traitsMERS-CoVstate-collapsed
state-collapsed-tree-earliest
state collapsed tree earliest
traitsEbola virusstate-collapsed
state-collapsed-tree-earliest-adjust
state collapsed tree earliest adjust
traitsEbola virusstate-collapsed
state-collapsed-tree-earliest-adjust
state collapsed tree earliest adjust
traitsMERS-CoVstate-collapsed

Time and dating

height-95HPD-bars
height 95HPD bars
time-scaledEbola virusheight bars
height-95HPD-bars
height 95HPD bars
time-scaledMERS-CoVheight bars
root-to-tip
root to tip
root-to-tiptime-scaledZika virusscale bar
samogitia-ebola-tmrca
samogitia ebola tmrca
time-scaledEbola virusTMRCAposterior processing
tmrca-hpd-tree
tmrca hpd tree
time-scaledEbola virusTMRCA

Geography

map-tree
map tree
geographyWuMV-6
nextstrain-flu-lineage-map
nextstrain flu lineage map
geographynextstrainInfluenza B virus
nextstrain-measles-map-piecharts
nextstrain measles map piecharts
geographynextstrainMeasles virus
nextstrain-nipah-map-piecharts
nextstrain nipah map piecharts
geographynextstrainNipah virusconnectors

Reticulate evolution

nextstrain-avian-flu-tanglegram
nextstrain avian flu tanglegram
nextstrainInfluenza B virustanglegram
reassortment-network
reassortment network
reassortmentWuMV-6reassortment network
tangled-chain
tangled chain
Influenza B virustanglegram
tangled-chain
tangled chain
reassortmentWuMV-6tanglegram

Nextstrain

auspice-json-io
auspice json io
nextstrainAuspice JSONIO
nextstrain-avian-flu-tanglegram
nextstrain avian flu tanglegram
nextstrainInfluenza B virustanglegram
nextstrain-flu-lineage-map
nextstrain flu lineage map
geographynextstrainInfluenza B virus
nextstrain-measles-map-piecharts
nextstrain measles map piecharts
geographynextstrainMeasles virus
nextstrain-nipah-map-piecharts
nextstrain nipah map piecharts
geographynextstrainNipah virusconnectors

Special visualisations

gradient-clade
gradient clade
traitsMERS-CoVgradient clade
Muller-plot-abstract
Muller plot abstract
MullerSARS-CoV-2
skygrid-calendar-time
skygrid calendar time
time-scaledMERS-CoVskygrid
skygrid-relative-time
skygrid relative time
time-scaledMERS-CoVskygrid
snp-alignment
snp alignment
SARS-CoV-2SNP alignment
travel-aware-tree
travel aware tree
SARS-CoV-2travel-aware

Utilities

auspice-json-io
auspice json io
nextstrainAuspice JSONIO
pad-nodes
pad nodes
MERS-CoVpad nodes
samogitia-ebola-custom
samogitia ebola custom
Ebola virusposterior processing
samogitia-ebola-tmrca
samogitia ebola tmrca
time-scaledEbola virusTMRCAposterior processing
samogitia-rabv-trace-state
samogitia rabv trace state
traitsRabies virusposterior processing
tree-matrix
tree matrix
Influenza B virusmatrix
tree-matrix
tree matrix
WuMV-6matrix

Custom visualisations

homoplasy-tree
homoplasy tree
MERS-CoVhomoplasy