Merge pull request #122 from nextstrain/figure-in-readmes

Add clade figures to SC2 readmes

data/nextstrain/sars-cov-2/BA.2.86/README.md

@@ -30,6 +30,20 @@ This dataset supports:
 - Phylogenetic placement
 - Calculation of ACE2 binding scores relative to BA.2.86 as described in [Starr et al. 2022](https://doi.org/10.1371/journal.ppat.1010951)
 
+## Nextstrain clades
+
+Since its emergence in late 2019, SARS-CoV-2 has evolved into many co-circulating variants. To facilitate discussion of these variants, we have grouped them into clades which are defined by specific signature mutations.
+
+Nextstrain clade names consist of two numbers representing a year and then a single letter representing the clade within that year. For example, 21A is the first clade we named in 2021.
+
+We define each clade by a combination of signature mutations. You can find the exact clade definition on Github in this [file](https://github.com/nextstrain/ncov/blob/master/defaults/clades.tsv).
+
+Below is an illustration of the phylogenetic relationships of Nextstrain clades ([source](https://github.com/nextstrain/ncov-clades-schema/)):
+
+![Illustration of phylogenetic relationships of SARS-CoV-2 clades, as defined by Nextstrain](https://raw.githubusercontent.com/nextstrain/ncov-clades-schema/master/clades.svg)
+
+Learn more about how Nextclade assigns clades in the [documentation](https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/).
+
 ## What are Nextclade datasets
 
 Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

data/nextstrain/sars-cov-2/BA.2/README.md

@@ -31,6 +31,20 @@ This dataset supports:
 - Calculation of immune escape scores relative to BA.2 neutralizing antibodies as described in [Greaney et al. 2022](https://doi.org/10.1093/ve/veac021)
 - Calculation of ACE2 binding scores relative to BA.2 as described in [Starr et al. 2022](https://doi.org/10.1371/journal.ppat.1010951)
 
+## Nextstrain clades
+
+Since its emergence in late 2019, SARS-CoV-2 has evolved into many co-circulating variants. To facilitate discussion of these variants, we have grouped them into clades which are defined by specific signature mutations.
+
+Nextstrain clade names consist of two numbers representing a year and then a single letter representing the clade within that year. For example, 21A is the first clade we named in 2021.
+
+We define each clade by a combination of signature mutations. You can find the exact clade definition on Github in this [file](https://github.com/nextstrain/ncov/blob/master/defaults/clades.tsv).
+
+Below is an illustration of the phylogenetic relationships of Nextstrain clades ([source](https://github.com/nextstrain/ncov-clades-schema/)):
+
+![Illustration of phylogenetic relationships of SARS-CoV-2 clades, as defined by Nextstrain](https://raw.githubusercontent.com/nextstrain/ncov-clades-schema/master/clades.svg)
+
+Learn more about how Nextclade assigns clades in the [documentation](https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/).
+
 ## What are Nextclade datasets
 
 Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

data/nextstrain/sars-cov-2/XBB/README.md

@@ -31,6 +31,20 @@ This dataset supports:
 - Calculation of immune escape scores relative to XBB neutralizing antibodies as described in [Greaney et al. 2022](https://doi.org/10.1093/ve/veac021)
 - Calculation of ACE2 binding scores relative to XBB as described in [Starr et al. 2022](https://doi.org/10.1371/journal.ppat.1010951)
 
+## Nextstrain clades
+
+Since its emergence in late 2019, SARS-CoV-2 has evolved into many co-circulating variants. To facilitate discussion of these variants, we have grouped them into clades which are defined by specific signature mutations.
+
+Nextstrain clade names consist of two numbers representing a year and then a single letter representing the clade within that year. For example, 21A is the first clade we named in 2021.
+
+We define each clade by a combination of signature mutations. You can find the exact clade definition on Github in this [file](https://github.com/nextstrain/ncov/blob/master/defaults/clades.tsv).
+
+Below is an illustration of the phylogenetic relationships of Nextstrain clades ([source](https://github.com/nextstrain/ncov-clades-schema/)):
+
+![Illustration of phylogenetic relationships of SARS-CoV-2 clades, as defined by Nextstrain](https://raw.githubusercontent.com/nextstrain/ncov-clades-schema/master/clades.svg)
+
+Learn more about how Nextclade assigns clades in the [documentation](https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/).
+
 ## What are Nextclade datasets
 
 Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/README.md

@@ -29,6 +29,20 @@ This dataset supports:
 - Sequence QC
 - Phylogenetic placement
 
+## Nextstrain clades
+
+Since its emergence in late 2019, SARS-CoV-2 has evolved into many co-circulating variants. To facilitate discussion of these variants, we have grouped them into clades which are defined by specific signature mutations.
+
+Nextstrain clade names consist of two numbers representing a year and then a single letter representing the clade within that year. For example, 21A is the first clade we named in 2021.
+
+We define each clade by a combination of signature mutations. You can find the exact clade definition on Github in this [file](https://github.com/nextstrain/ncov/blob/master/defaults/clades.tsv).
+
+Below is an illustration of the phylogenetic relationships of Nextstrain clades ([source](https://github.com/nextstrain/ncov-clades-schema/)):
+
+![Illustration of phylogenetic relationships of SARS-CoV-2 clades, as defined by Nextstrain](https://raw.githubusercontent.com/nextstrain/ncov-clades-schema/master/clades.svg)
+
+Learn more about how Nextclade assigns clades in the [documentation](https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/).
+
 ## What are Nextclade datasets
 
 Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

data/nextstrain/sars-cov-2/wuhan-hu-1/proteins/README.md

@@ -31,6 +31,20 @@ This dataset supports:
 - Sequence QC
 - Phylogenetic placement
 
+## Nextstrain clades
+
+Since its emergence in late 2019, SARS-CoV-2 has evolved into many co-circulating variants. To facilitate discussion of these variants, we have grouped them into clades which are defined by specific signature mutations.
+
+Nextstrain clade names consist of two numbers representing a year and then a single letter representing the clade within that year. For example, 21A is the first clade we named in 2021.
+
+We define each clade by a combination of signature mutations. You can find the exact clade definition on Github in this [file](https://github.com/nextstrain/ncov/blob/master/defaults/clades.tsv).
+
+Below is an illustration of the phylogenetic relationships of Nextstrain clades ([source](https://github.com/nextstrain/ncov-clades-schema/)):
+
+![Illustration of phylogenetic relationships of SARS-CoV-2 clades, as defined by Nextstrain](https://raw.githubusercontent.com/nextstrain/ncov-clades-schema/master/clades.svg)
+
+Learn more about how Nextclade assigns clades in the [documentation](https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/).
+
 ## What are Nextclade datasets
 
 Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/README.md

@@ -30,6 +30,20 @@ This dataset supports:
 - Phylogenetic placement
 - Calculation of ACE2 binding scores relative to BA.2.86 as described in [Starr et al. 2022](https://doi.org/10.1371/journal.ppat.1010951)
 
+## Nextstrain clades
+
+Since its emergence in late 2019, SARS-CoV-2 has evolved into many co-circulating variants. To facilitate discussion of these variants, we have grouped them into clades which are defined by specific signature mutations.
+
+Nextstrain clade names consist of two numbers representing a year and then a single letter representing the clade within that year. For example, 21A is the first clade we named in 2021.
+
+We define each clade by a combination of signature mutations. You can find the exact clade definition on Github in this [file](https://github.com/nextstrain/ncov/blob/master/defaults/clades.tsv).
+
+Below is an illustration of the phylogenetic relationships of Nextstrain clades ([source](https://github.com/nextstrain/ncov-clades-schema/)):
+
+![Illustration of phylogenetic relationships of SARS-CoV-2 clades, as defined by Nextstrain](https://raw.githubusercontent.com/nextstrain/ncov-clades-schema/master/clades.svg)
+
+Learn more about how Nextclade assigns clades in the [documentation](https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/).
+
 ## What are Nextclade datasets
 
 Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

data_output/nextstrain/sars-cov-2/BA.2/unreleased/README.md

@@ -31,6 +31,20 @@ This dataset supports:
 - Calculation of immune escape scores relative to BA.2 neutralizing antibodies as described in [Greaney et al. 2022](https://doi.org/10.1093/ve/veac021)
 - Calculation of ACE2 binding scores relative to BA.2 as described in [Starr et al. 2022](https://doi.org/10.1371/journal.ppat.1010951)
 
+## Nextstrain clades
+
+Since its emergence in late 2019, SARS-CoV-2 has evolved into many co-circulating variants. To facilitate discussion of these variants, we have grouped them into clades which are defined by specific signature mutations.
+
+Nextstrain clade names consist of two numbers representing a year and then a single letter representing the clade within that year. For example, 21A is the first clade we named in 2021.
+
+We define each clade by a combination of signature mutations. You can find the exact clade definition on Github in this [file](https://github.com/nextstrain/ncov/blob/master/defaults/clades.tsv).
+
+Below is an illustration of the phylogenetic relationships of Nextstrain clades ([source](https://github.com/nextstrain/ncov-clades-schema/)):
+
+![Illustration of phylogenetic relationships of SARS-CoV-2 clades, as defined by Nextstrain](https://raw.githubusercontent.com/nextstrain/ncov-clades-schema/master/clades.svg)
+
+Learn more about how Nextclade assigns clades in the [documentation](https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/).
+
 ## What are Nextclade datasets
 
 Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

data_output/nextstrain/sars-cov-2/XBB/unreleased/README.md

@@ -31,6 +31,20 @@ This dataset supports:
 - Calculation of immune escape scores relative to XBB neutralizing antibodies as described in [Greaney et al. 2022](https://doi.org/10.1093/ve/veac021)
 - Calculation of ACE2 binding scores relative to XBB as described in [Starr et al. 2022](https://doi.org/10.1371/journal.ppat.1010951)
 
+## Nextstrain clades
+
+Since its emergence in late 2019, SARS-CoV-2 has evolved into many co-circulating variants. To facilitate discussion of these variants, we have grouped them into clades which are defined by specific signature mutations.
+
+Nextstrain clade names consist of two numbers representing a year and then a single letter representing the clade within that year. For example, 21A is the first clade we named in 2021.
+
+We define each clade by a combination of signature mutations. You can find the exact clade definition on Github in this [file](https://github.com/nextstrain/ncov/blob/master/defaults/clades.tsv).
+
+Below is an illustration of the phylogenetic relationships of Nextstrain clades ([source](https://github.com/nextstrain/ncov-clades-schema/)):
+
+![Illustration of phylogenetic relationships of SARS-CoV-2 clades, as defined by Nextstrain](https://raw.githubusercontent.com/nextstrain/ncov-clades-schema/master/clades.svg)
+
+Learn more about how Nextclade assigns clades in the [documentation](https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/).
+
 ## What are Nextclade datasets
 
 Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/README.md

@@ -29,6 +29,20 @@ This dataset supports:
 - Sequence QC
 - Phylogenetic placement
 
+## Nextstrain clades
+
+Since its emergence in late 2019, SARS-CoV-2 has evolved into many co-circulating variants. To facilitate discussion of these variants, we have grouped them into clades which are defined by specific signature mutations.
+
+Nextstrain clade names consist of two numbers representing a year and then a single letter representing the clade within that year. For example, 21A is the first clade we named in 2021.
+
+We define each clade by a combination of signature mutations. You can find the exact clade definition on Github in this [file](https://github.com/nextstrain/ncov/blob/master/defaults/clades.tsv).
+
+Below is an illustration of the phylogenetic relationships of Nextstrain clades ([source](https://github.com/nextstrain/ncov-clades-schema/)):
+
+![Illustration of phylogenetic relationships of SARS-CoV-2 clades, as defined by Nextstrain](https://raw.githubusercontent.com/nextstrain/ncov-clades-schema/master/clades.svg)
+
+Learn more about how Nextclade assigns clades in the [documentation](https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/).
+
 ## What are Nextclade datasets
 
 Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/README.md

@@ -31,6 +31,20 @@ This dataset supports:
 - Sequence QC
 - Phylogenetic placement
 
+## Nextstrain clades
+
+Since its emergence in late 2019, SARS-CoV-2 has evolved into many co-circulating variants. To facilitate discussion of these variants, we have grouped them into clades which are defined by specific signature mutations.
+
+Nextstrain clade names consist of two numbers representing a year and then a single letter representing the clade within that year. For example, 21A is the first clade we named in 2021.
+
+We define each clade by a combination of signature mutations. You can find the exact clade definition on Github in this [file](https://github.com/nextstrain/ncov/blob/master/defaults/clades.tsv).
+
+Below is an illustration of the phylogenetic relationships of Nextstrain clades ([source](https://github.com/nextstrain/ncov-clades-schema/)):
+
+![Illustration of phylogenetic relationships of SARS-CoV-2 clades, as defined by Nextstrain](https://raw.githubusercontent.com/nextstrain/ncov-clades-schema/master/clades.svg)
+
+Learn more about how Nextclade assigns clades in the [documentation](https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/).
+
 ## What are Nextclade datasets
 
 Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html