Examples

This page showcases real-world examples using published phylogenetic datasets.

Weisberg et al. 2020

Phylogenetic trees of Agrobacterium isolates from a study on virulence plasmid conservation and transmission:

Alexandra J. Weisberg et al., Unexpected conservation and global transmission of agrobacterial virulence plasmids. Science 368, eaba5256 (2020).

The widget below contains both the MLSA (multilocus sequence analysis) tree and the time-calibrated BEAST tree. Use the “Select tree” dropdown in the toolbar’s “Data” tab to switch between them.

from heattree_py import heat_tree, example_data

heat_tree(
    tree=[
        example_data("weisberg_2020_mlsa"),
        example_data("weisberg_2020_beast")
    ],
    metadata=[
        example_data("weisberg_2020_metadata"),
        example_data("weisberg_2020_metadata")
    ],
    aesthetics=[
        {"tipLabelText": "strain", "tipLabelColor": "host_type"},
        {"tipLabelText": "strain", "tipLabelColor": "year_isolated"}
    ],
    tree_names=["MLSA", "BEAST"],
    layout="circular"
)

Bansal et al. 2021

Phylogenetic tree 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.

heat_tree(
    example_data("bansal_2021_tree"),
    metadata=example_data("bansal_2021_metadata"),
    aesthetics={
        "tipLabelText": "Strain",
        "tipLabelColor": "Lifestyle"
    }
)