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Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2
https://doi.org/10.1101/2024.02.07.579374
MIT License
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Rerun PCA with simplex encoding of sequences #116

Closed huddlej closed 2 months ago

huddlej commented 3 months ago

Description

Updates results for PCA and t-SNE using the simplex encoding of sequences in alignments.

Development checklist

  1. [x] Setup environment to install pathogen-embed 2.1.0
  2. [x] Add flag to encode PCA and t-SNE inputs with simplex to all workflows
  3. [x] Delete PCA and t-SNE output files for all populations
  4. [x] Re-run workflow for all outputs related to PCA and t-SNE
  5. [x] Update manuscript text to reflect new method and results

Related issues

Closes #115