The idea behind TreeSort is the observation that if there is no reassortment, then the evolutionary histories of different segments should be identical. TreeSort then uses a phylogenetic tree for one segment (e.g., the HA influenza A virus segment) as an evolutionary hypothesis for another segment (e.g., the NA segment). We will refer to the first segment as the reference and the second segment as the challenge. By trying to fit the sequence alignment of the challenge segment to the reference tree, TreeSort identifies points on that tree, where this evolutionary hypothesis breaks. The "breaking" manifests in the mismatch between the divergence time on the reference tree (e.g., 1 year divergence between sister clades) and an unlikely high number of substitutions in the challenge segment that are required to explain the reference tree topology under the null hypothesis of no reassortment.
TreeSort has demonstrated very high accuracy in reassortment inference in simulations (manuscript in preparation). TreeSort can process datasets with tens of thousands of virus strains in just a few minutes and can scale to very large datasets with hundreds of thousands of strains. (This overview is from https://github.com/flu-crew/TreeSort/blob/main/README.md)
This module is a component of the BV-BRC build system. It is designed to fit into the
dev_container infrastructure which manages development and production deployment of
the components of the BV-BRC. More documentation is available here.
There is one application service specification defined here:
- TreeSort: The TreeSort tool infers both recent and ancestral reassortment events along the branches of a phylogenetic tree of a fixed genomic segment. It uses a statistical hypothesis testing framework to identify branches where reassortment with other segments has occurred and reports these events.
The code in this module provides the BV-BRC application service wrapper scripts for the TreeSort service as well as some backend utilities:
| Script name | Purpose |
|---|---|
| App-TreeSort.pl | App script for the TreeSort service |
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Alexey Markin, Catherine A. Macken, Amy L. Baker, Tavis K. Anderson, "Revealing reassortment in influenza A viruses with TreeSort" bioRxiv 2024.11.15.623781; doi: https://doi.org/10.1101/2024.11.15.623781