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Expand Up @@ -68,29 +68,27 @@ Explore the phylogenetic trees and embeddings on Nextstrain.

## Interactive figures

- [Fig 2. **Phylogeny of early (2016–2018) influenza H3N2 HA sequences plotted by nucleotide substitutions per site on the x-axis (top) and low-dimensional embeddings of the same sequences by PCA (middle left), MDS (middle right), t-SNE (bottom left), and UMAP (bottom right).** Tips in the tree and embeddings are colored by their Nextstrain clade assignment.](https://blab.github.io/cartography/figures/flu-2016-2018-ha-embeddings-by-clade.html)
- [**MDS embeddings for early (2016–2018) influenza H3N2 HA sequences showing all three components.**](https://blab.github.io/cartography/figures/flu-2016-2018-mds-by-clade.html)
- [Fig 4. **Phylogenetic trees (left) and embeddings (right) of early (2016–2018) influenza H3N2 HA sequences colored by HDBSCAN cluster.** Normalized VI values per embedding reflect the distance between clusters and known genetic groups
(Nextstrain clades).](https://blab.github.io/cartography/figures/flu-2016-2018-ha-embeddings-by-cluster.html)
- [S5 Fig. **Phylogeny of late (2018–2020) influenza H3N2 HA sequences plotted by nucleotide substitutions per site on the x-axis (top) and low-dimensional embeddings of the same sequences by PCA (middle left), MDS (middle right), t-SNE (bottom left), and UMAP (bottom right).** Tips in the tree and embeddings are colored by their Nextstrain clade assignment.](https://blab.github.io/cartography/figures/flu-2018-2020-ha-embeddings-by-clade.html)
- [S6 Fig. **MDS embeddings for late (2018–2020) influenza H3N2 HA sequences showing all three components.**](https://blab.github.io/cartography/figures/flu-2018-2020-mds-by-clade.html)
- [Fig 5. **Phylogenetic trees (left) and embeddings (right) of late (2018–2020) H3N2 HA sequences colored by HDBSCAN cluster.** Normalized VI values per embedding reflect the distance between clusters and known genetic groups (Nextstrain clades).](https://blab.github.io/cartography/figures/flu-2018-2020-ha-embeddings-by-cluster.html)
- [Fig 6. **Phylogeny of early (2016–2018) influenza H3N2 HA sequences plotted by nucleotide substitutions per site on the x-axis (top) and low-dimensional embeddings of the same HA sequences concatenated with matching NA sequences by PCA (middle left), MDS (middle right), t-SNE (bottom left), and UMAP (bottom right).** Tips in the tree and embeddings are colored by their TreeKnit Maximally Compatible Clades (MCCs) label which represents putative HA/NA reassortment groups. The first normalized VI values per embedding reflect the distance between HA/NA clusters and known genetic groups (MCCs). VI values in parentheses reflect the distance between HA-only clusters and known genetic groups.](https://blab.github.io/cartography/figures/flu-2016-2018-ha-na-embeddings-by-mcc.html)
- [S8 Fig. **Embeddings influenza H3N2 HA-only (left) and combined HA/NA (right) showing the effects of additional NA genetic information on the
- [Fig 2. **Phylogeny of early (2016–2018) influenza H3N2 HA sequences plotted by nucleotide substitutions per site on the x-axis (top) and low-dimensional embeddings of the same sequences by PCA (middle left), MDS (middle right), t-SNE (bottom left), and UMAP (bottom right).**](https://blab.github.io/cartography/figures/flu-2016-2018-ha-embeddings-by-clade.html) Tips in the tree and embeddings are colored by their Nextstrain clade assignment.
- [S4 Fig. **MDS embeddings for early (2016–2018) influenza H3N2 HA sequences showing all three components.**](https://blab.github.io/cartography/figures/flu-2016-2018-mds-by-clade.html)
- [Fig 4. **Phylogenetic trees (left) and embeddings (right) of early (2016–2018) influenza H3N2 HA sequences colored by HDBSCAN cluster.**](https://blab.github.io/cartography/figures/flu-2016-2018-ha-embeddings-by-cluster.html) Normalized VI values per embedding reflect the distance between clusters and known genetic groups
(Nextstrain clades).
- [S6 Fig. **Phylogeny of late (2018–2020) influenza H3N2 HA sequences plotted by nucleotide substitutions per site on the x-axis (top) and low-dimensional embeddings of the same sequences by PCA (middle left), MDS (middle right), t-SNE (bottom left), and UMAP (bottom right).**](https://blab.github.io/cartography/figures/flu-2018-2020-ha-embeddings-by-clade.html) Tips in the tree and embeddings are colored by their Nextstrain clade assignment.
- [S7 Fig. **MDS embeddings for late (2018–2020) influenza H3N2 HA sequences showing all three components.**](https://blab.github.io/cartography/figures/flu-2018-2020-mds-by-clade.html)
- [Fig 5. **Phylogenetic trees (left) and embeddings (right) of late (2018–2020) H3N2 HA sequences colored by HDBSCAN cluster.**](https://blab.github.io/cartography/figures/flu-2018-2020-ha-embeddings-by-cluster.html) Normalized VI values per embedding reflect the distance between clusters and known genetic groups (Nextstrain clades).
- [Fig 6. **Phylogeny of early (2016–2018) influenza H3N2 HA sequences plotted by nucleotide substitutions per site on the x-axis (top) and low-dimensional embeddings of the same HA sequences concatenated with matching NA sequences by PCA (middle left), MDS (middle right), t-SNE (bottom left), and UMAP (bottom right).**](https://blab.github.io/cartography/figures/flu-2016-2018-ha-na-embeddings-by-mcc.html) Tips in the tree and embeddings are colored by their TreeKnit Maximally Compatible Clades (MCCs) label which represents putative HA/NA reassortment groups. The first normalized VI values per embedding reflect the distance between HA/NA clusters and known genetic groups (MCCs). VI values in parentheses reflect the distance between HA-only clusters and known genetic groups.
- [S9 Fig. **Embeddings influenza H3N2 HA-only (left) and combined HA/NA (right) showing the effects of additional NA genetic information on the
placement of reassortment events detected by TreeKnit (MCCs).**](https://blab.github.io/cartography/figures/flu-2016-2018-ha-na-all-embeddings-by-mcc.html)
- [S9 Fig. **PCA embeddings for influenza H3N2 HA sequences only (top row) and HA/NA sequences combined (bottom row) showing the HA trees colored by clusters identified in each embedding (left) and the corresponding embeddings colored by cluster (right).**](https://blab.github.io/cartography/figures/flu-2016-2018-ha-na-pca-by-cluster.html)
- [S10 Fig. **MDS embeddings for influenza H3N2 HA sequences only (top row) and HA/NA sequences combined (bottom row) showing the HA trees colored by clusters identified in each embedding (left) and the corresponding embeddings colored by cluster (right).**](https://blab.github.io/cartography/figures/flu-2016-2018-ha-na-mds-by-cluster.html)
- [S11 Fig. **t-SNE embeddings for influenza H3N2 HA sequences only (top row) and HA/NA sequences combined (bottom row) showing the HA trees colored by clusters identified in each embedding (left) and the corresponding embeddings colored by cluster (right).**](https://blab.github.io/cartography/figures/flu-2016-2018-ha-na-tsne-by-cluster.html)
- [S12 Fig. **UMAP embeddings for influenza H3N2 HA sequences only (top row) and HA/NA sequences combined (bottom row) showing the HA trees colored by clusters identified in each embedding (left) and the corresponding embeddings colored by cluster (right).**](https://blab.github.io/cartography/figures/flu-2016-2018-ha-na-umap-by-cluster.html)
- [Fig 7. **Phylogeny of early (2020–2022) SARS-CoV-2 sequences plotted by number of nucleotide substitutions from the most recent common ancestor on the x-axis (top) and low-dimensional embeddings of the same sequences by PCA (middle left), MDS (middle right), t-SNE (bottom left), and UMAP (bottom right).** Tips in the tree and embeddings are colored by their Nextstrain clade assignment.](https://blab.github.io/cartography/figures/sarscov2-embeddings-by-Nextstrain_clade-clade.html)
- [S13 Fig. **MDS embeddings for early SARS-CoV-2 sequences showing all three components.**](https://blab.github.io/cartography/figures/sarscov2-mds-by-Nextstrain_clade-clade.html)
- [S15 Fig. **Phylogeny of early (2020–2022) SARS-CoV-2 sequences plotted by number of nucleotide substitutions from the most recent common ancestor on the x-axis (top) and low-dimensional embeddings of the same sequences by PCA (middle left), MDS (middle right), t-SNE (bottom left), and UMAP (bottom right).** Tips in the tree and embeddings are colored by their collapsed Nextclade pango lineage assignment.](https://blab.github.io/cartography/figures/sarscov2-embeddings-by-Nextclade_pango_collapsed-clade.html)
- [Fig 9. **Phylogenetic trees (left) and embeddings (right) of early (2020–2022) SARS-CoV-2 sequences colored by HDBSCAN cluster. Normalized VI values per embedding reflect the distance between clusters and known genetic groups
(Nextstrain clades).**](https://blab.github.io/cartography/figures/sarscov2-embeddings-by-cluster-vs-Nextstrain_clade.html)
- [S17 Fig. **Phylogenetic trees (left) and embeddings (right) of early (2020–2022) SARS-CoV-2 sequences colored by HDBSCAN cluster.** Normalized VI values per embedding reflect the distance between clusters and known genetic groups (collapsed Nextclade pango lineages).](https://blab.github.io/cartography/figures/sarscov2-embeddings-by-cluster-vs-Nextclade_pango_collapsed.html)
- [Fig 10. **Phylogenetic trees (left) and embeddings (right) of late (2022–2023) SARS-CoV-2 sequences colored by HDBSCAN cluster.** Normalized VI values per embedding reflect the distance between clusters and known genetic groups
(Nextstrain clades).](https://blab.github.io/cartography/figures/sarscov2-test-embeddings-by-cluster-vs-Nextstrain_clade.html)
- [S19 Fig. **Phylogenetic trees (left) and embeddings (right) of late (2022–2023) SARS-CoV-2 sequences colored by HDBSCAN cluster.** Normalized VI values per embedding reflect the distance between clusters and known genetic groups (collapsed Nextclade pango lineages).](https://blab.github.io/cartography/figures/sarscov2-test-embeddings-by-cluster-vs-Nextclade_pango_collapsed.html)
- [S10 Fig. **PCA embeddings for influenza H3N2 HA sequences only (top row) and HA/NA sequences combined (bottom row) showing the HA trees colored by clusters identified in each embedding (left) and the corresponding embeddings colored by cluster (right).**](https://blab.github.io/cartography/figures/flu-2016-2018-ha-na-pca-by-cluster.html)
- [S11 Fig. **MDS embeddings for influenza H3N2 HA sequences only (top row) and HA/NA sequences combined (bottom row) showing the HA trees colored by clusters identified in each embedding (left) and the corresponding embeddings colored by cluster (right).**](https://blab.github.io/cartography/figures/flu-2016-2018-ha-na-mds-by-cluster.html)
- [S12 Fig. **t-SNE embeddings for influenza H3N2 HA sequences only (top row) and HA/NA sequences combined (bottom row) showing the HA trees colored by clusters identified in each embedding (left) and the corresponding embeddings colored by cluster (right).**](https://blab.github.io/cartography/figures/flu-2016-2018-ha-na-tsne-by-cluster.html)
- [S13 Fig. **UMAP embeddings for influenza H3N2 HA sequences only (top row) and HA/NA sequences combined (bottom row) showing the HA trees colored by clusters identified in each embedding (left) and the corresponding embeddings colored by cluster (right).**](https://blab.github.io/cartography/figures/flu-2016-2018-ha-na-umap-by-cluster.html)
- [Fig 7. **Phylogeny of early (2020–2022) SARS-CoV-2 sequences plotted by number of nucleotide substitutions from the most recent common ancestor on the x-axis (top) and low-dimensional embeddings of the same sequences by PCA (middle left), MDS (middle right), t-SNE (bottom left), and UMAP (bottom right).**](https://blab.github.io/cartography/figures/sarscov2-embeddings-by-Nextstrain_clade-clade.html) Tips in the tree and embeddings are colored by their Nextstrain clade assignment.
- [S14 Fig. **MDS embeddings for early SARS-CoV-2 sequences showing all three components.**](https://blab.github.io/cartography/figures/sarscov2-mds-by-Nextstrain_clade-clade.html)
- [S16 Fig. **Phylogeny of early (2020–2022) SARS-CoV-2 sequences plotted by number of nucleotide substitutions from the most recent common ancestor on the x-axis (top) and low-dimensional embeddings of the same sequences by PCA (middle left), MDS (middle right), t-SNE (bottom left), and UMAP (bottom right).**](https://blab.github.io/cartography/figures/sarscov2-embeddings-by-Nextclade_pango_collapsed-clade.html) Tips in the tree and embeddings are colored by their collapsed Nextclade pango lineage assignment.
- [Fig 9. **Phylogenetic trees (left) and embeddings (right) of early (2020–2022) SARS-CoV-2 sequences colored by HDBSCAN cluster.**](https://blab.github.io/cartography/figures/sarscov2-embeddings-by-cluster-vs-Nextstrain_clade.html) Normalized VI values per embedding reflect the distance between clusters and known genetic groups (Nextstrain clades).
- [S18 Fig. **Phylogenetic trees (left) and embeddings (right) of early (2020–2022) SARS-CoV-2 sequences colored by HDBSCAN cluster.**](https://blab.github.io/cartography/figures/sarscov2-embeddings-by-cluster-vs-Nextclade_pango_collapsed.html) Normalized VI values per embedding reflect the distance between clusters and known genetic groups (collapsed Nextclade pango lineages).
- [Fig 10. **Phylogenetic trees (left) and embeddings (right) of late (2022–2023) SARS-CoV-2 sequences colored by HDBSCAN cluster.**](https://blab.github.io/cartography/figures/sarscov2-test-embeddings-by-cluster-vs-Nextstrain_clade.html) Normalized VI values per embedding reflect the distance between clusters and known genetic groups (Nextstrain clades).
- [S20 Fig. **Phylogenetic trees (left) and embeddings (right) of late (2022–2023) SARS-CoV-2 sequences colored by HDBSCAN cluster.**](https://blab.github.io/cartography/figures/sarscov2-test-embeddings-by-cluster-vs-Nextclade_pango_collapsed.html) Normalized VI values per embedding reflect the distance between clusters and known genetic groups (collapsed Nextclade pango lineages).

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