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Visualizing PhyloPHoeNIx Output

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Jill V. Hagey, PhD edited this page Nov 26, 2024 · 5 revisions

PhyloPHoeNIx output seamlessly integrates into Microreact through their upload portal. There are up to 3 files you can upload directly from PhyloPHoeNIx output folder to Microreact:

  1. <ST>_clean_metadata.tsv
  2. <ST>_phylogeneticTree.newick
  3. <ST>_snvMatrix.tsv

Make sure you set the matrix to matrix so MicroReact knows how to handle it.

DISCLAIMER: The methods used for phylogenetic determination and the data summarized are for public health surveillance or investigational purposes only and must NOT be communicated to the patient, their care provider, or placed in the patient’s medical record. These results should NOT be used for diagnosis, treatment, or assessment of individual patient health or management.

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