Dataset
community
ViennaRNA
CHIKV
Date Range
Use this slider to filter the data based on the sample date. This may include inferred dates for ancestral nodes in the tree, and thus the date range here can be wider than the sample collection range.
1698-01-01
2022-07-28
Color By
Change the metadata field which the visualisation is coloured by.
The phylogeny, map and frequencies panel (if available) will all be coloured in a consistent fashion.
Lineage
Filter Data
Use this box to filter the displayed data based upon filtering criteria. For instance, start typing a country's name to filter the data accordingly.
Data is filtered by forming a union of selected values within each category, and then taking the intersection between categories (if more than one category is selected).
Scroll to the bottom of the main page (under the data visualisation) to see an expanded display of filters and available values.
Filter options prefixed with "(M)" are filters specific to the Measurements panel. They will have no effect on the phylogeny tree or other panels.
Type filter query here...
Tree
This panel displays the evolutionary relationships among samples, illustrating their genetic relatedness and inferred ancestry.
The exact options available depend on the dataset and specific analysis performed.
If Branch Length is available, you can choose to display the tree branches in terms of (nucleotide) divergence or (inferred) time. It is often helpful to toggle on confidence intervals to gauge the uncertainty in the reconstruction of internal node dates.
Layout
Branch Length
Branch Labels
none
Tip Labels
Sample Name
Explode Tree By
Exploding a tree by trait X means that for each branch where the trait changes value, we will prune off the branch and create a separate (sub)tree. It works best when the trait doesn't change value too frequently.
Select...
Map
This panel displays the geographical distribution of samples.
The geographic resolution chooses the metadata values which define where samples are placed on the map. This can be the same as the selected color-by but is often not!
Geographic resolution
country
Entropy
This panel displays the observed diversity across the current genome or a selected CDS. All options are in the panel itself.
Animation Options
Change various options relating to how the animation proceeds.
Animation Speed

Display
Control whether to show the tree and the map side-by-side (grid) or expanded (full).
Language
English
CHIKVnext: Molecular epidemiology of Chikungunya virus
Built with . Maintained by Thomas Spicher, Markus Delitz, , and . Data updated 2023-01-06.
Showing 1398 of 1398 genomes sampled between Feb 1953 and Jul 2022.
Phylogeny
AUL-AmAUL-AmAULAULWAWAAfrican/Asian LineagesAfrican/Asian LineagesSister Taxa to ECSASister Taxa to ECSAIOLIOLEALEALMALMALSALSALLineage169517351775181518551895193519752015Date
Transmissions
AUL-AmAUL-AmAULAULWAWAAfrican/Asian LineagesAfrican/Asian LineagesSister Taxa to ECSASister Taxa to ECSAIOLIOLEALEALMALMALSALSALLineage
Nucleotide diversity of genome
CHIKVgp1CHIKVgp2CHIKVgp1CHIKVgp20.00.20.40.60.81.0010002000300040005000600070008000900010000110001200005001,0001,5002,0002,5003,0003,5004,0004,5005,0005,5006,0006,5007,0007,5008,0008,5009,0009,50010,00010,50011,00011,50012,000
This panel displays the observed diversity across the current genome or a selected CDS (currently you are viewing the genome).

The lower axis shows the genome with +ve strand CDSs above and -ve strand CDSs below and the grey overlay allows zooming in to a region. The upper axis shows either the zoomed in region of the genome or a selected CDS; in the latter case the coordinates represent amino acids.

Clicking on a CDS will select it and show it on the upper axis. Clicking "Reset Layout" will always return you to viewing the entire genome.
Data updated 2023-01-06Auspice v2.63.1
Powered by Nextstrain (Hadfield et al Bioinformatics)