Chronologies from monumental phylogenetic trees
Chronumental is a tool for creating a "time-tree" (where distance on the tree represents time) from a phylogenetic divergence-tree (where distance on the tree reflects a number of genetic substitutions).
What sets Chronumental apart from most other tools is that it scales to extremely large trees, which can contain millions of nodes. Chronumental uses JAX to represent the task of computing a time tree in a differentiable graph for efficient calculation on a CPU or GPU.
pip install --local pipx
pipx install chronumental
pip install chronumental
Chronumental is now available on bioconda
conda config --add channels bioconda
conda install chronumental
This demo uses trees and metadata collated by the UShER team.
wget https://hgwdev.gi.ucsc.edu/~angie/UShER_SARS-CoV-2/2021/10/06/public-2021-10-06.all.nwk.gz
wget https://hgwdev.gi.ucsc.edu/~angie/UShER_SARS-CoV-2/2021/10/06/public-2021-10-06.metadata.tsv.gz
chronumental --tree public-2021-10-06.all.nwk.gz --dates public-2021-10-06.metadata.tsv.gz --steps 100
📚 Please visit our documentation page to learn more about the parameters you can use to control Chronumental.
Taxonium can automatically call Chronumental, and generate a combined visualisation that allows switching between distance and time phylogenies
TreeTime is a more advanced tool for inferring time trees. If you have a dataset of e.g. <10,000 rather than millions of nodes you are definitely best off trying it. The TreeTime readme also links to other similar tools.
- Chronumental uses the earliest date in your dataset as an anchor to calibrate everything else. If this earliest date is wrong due to a metadata error things won't work well. You can set the reference node manually with
--reference_nodeto avoid this issue.