Examples
This page showcases real-world examples using published phylogenetic datasets.
Weisberg et al. 2020
Below are two phylogenetic trees of agrobacteria isolates, one a multilocus sequence analysis (MLSA) and another from a time-calibrated BEAST tree, both from:
Alexandra J. Weisberg et al., Unexpected conservation and global transmission of agrobacterial virulence plasmids. Science 368, eaba5256 (2020)
<!DOCTYPE html>
<div id="container" style="width:100%;height:100vh;"></div>
<script type="module">
import { heatTree } from 'https://esm.sh/@grunwaldlab/heat-tree';
const mlsaTree = await fetch('https://raw.githubusercontent.com/grunwaldlab/heat-tree/dev/docs/public/data/weisberg_2020_mlsa.tre');
const beastTree = await fetch('https://raw.githubusercontent.com/grunwaldlab/heat-tree/dev/docs/public/data/weisberg_2020_beast.tre');
const metadata = await fetch('https://raw.githubusercontent.com/grunwaldlab/heat-tree/dev/docs/public/data/weisberg_2020_metadata.tsv');
const metaText = await metadata.text();
heatTree('#container',
[
{
name: 'MLSA',
tree: await mlsaTree.text(),
metadata: [{ name: 'Strain Metadata', data: metaText }],
aesthetics: {
tipLabelText: 'strain',
tipLabelColor: 'host_type'
}
},
{
name: 'BEAST',
tree: await beastTree.text(),
metadata: [{ name: 'Strain Metadata', data: metaText }],
aesthetics: {
tipLabelText: 'strain',
tipLabelColor: 'year_isolated'
}
}
],
{
layout: 'circular',
manualZoomAndPanEnabled: false
}
);
</script>Use the "Select tree" dropdown in the toolbar's "Data" tab to switch between the MLSA and BEAST trees.
Bansal et al. 2021
This example uses phylogenetic trees from a comparative genomics study of Xylella:
Bansal, K., Kumar, S., Kaur, A., Singh, A., & Patil, P. B. (2021). Deep phylo-taxono genomics reveals Xylella as a variant lineage of plant associated Xanthomonas and supports their taxonomic reunification along with Stenotrophomonas and Pseudoxanthomonas. Genomics, 113(6), 3989-4003.
<!DOCTYPE html>
<div id="container" style="width:100%;height:100vh;"></div>
<script type="module">
import { heatTree } from 'https://esm.sh/@grunwaldlab/heat-tree';
const tree = await fetch('https://raw.githubusercontent.com/grunwaldlab/heat-tree/dev/docs/public/data/bansal_2021_tree.nwk');
const metadata = await fetch('https://raw.githubusercontent.com/grunwaldlab/heat-tree/dev/docs/public/data/bansal_2021_metadata.tsv');
heatTree('#container',
{
name: 'Xylella Tree',
tree: await tree.text(),
metadata: [{ name: 'Strain Metadata', data: await metadata.text() }],
aesthetics: {
tipLabelText: 'Strain',
tipLabelColor: 'Lifestyle'
}
},
{
manualZoomAndPanEnabled: false
}
);
</script>