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Deep Learning for Phylogenetic Placement (DEPP)
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Classroom Contents
Distance-Based Phylogenetics: Past, Present, and Future - CGSI 2022
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- 1 Intro
- 2 A (weighted) tree defines a metric space
- 3 An additive metric space
- 4 How to get distances: Hamming distance?
- 5 Statistical distance correction
- 6 Inferring a tree from additive distances (the naive quartet approach)
- 7 Practical methods
- 8 Remarkably strong asymptotic theoretical results
- 9 Phylogenetic Placement (PP)
- 10 Application: ecological sample identification (e.g., microbiome)
- 11 Sample identification using genome skimming
- 12 Two-step summary methods
- 13 Deep Learning for Phylogenetic Placement (DEPP)
- 14 Food for thought
- 15 Questions?
