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aofarrel merged 1 commit into from
Jul 7, 2026
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Fix spelling #60

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2 changes: 1 addition & 1 deletion README.md
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# Tree Nine
The Tree Nine system is the basis of a tuberculosis cluster tracker built with funding from the California Department of Health, but it can also be run as a standalone workflow to simply place samples on an existing phylogenetic tree using [UShER](https://www.nature.com/articles/s41588-021-00862-7). For CDPH's TB cluster tracker, this system runs on Terra, but like any WDL workflow it can run on basically anything that supports Docker (Singularity is untested). We have verified compataibility with both Cromwell and miniwdl.
The Tree Nine system is the basis of a tuberculosis cluster tracker built with funding from the California Department of Health, but it can also be run as a standalone workflow to simply place samples on an existing phylogenetic tree using [UShER](https://www.nature.com/articles/s41588-021-00862-7). For CDPH's TB cluster tracker, this system runs on Terra, but like any WDL workflow it can run on basically anything that supports Docker (Singularity is untested). We have verified compatibility with both Cromwell and miniwdl.

If clustering is enabled, samples' SNP distance from each other is calculated from branch length, allowing them to be placed into clusters. Clustering can be done on a subset of samples or across the entire tree. Every run of Tree Nine with clustering outputs files with cluster information; if you put those files back into Tree Nine again, you can track changes to your clusters over time, maintaining persistent cluster IDs the entire time. Every cluster can optionally generate a Microreact template JSON and communicate with the Microreact API to automatically create projects containing the cluster's subtree, distance matrix, links to parent/subclusters, and a sample-level metadata table.

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