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Tidy a few ARG typos etc.
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args.md

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@@ -99,9 +99,9 @@ trees. However, all tree sequences can also be
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{ref}`plotted as graphs<sec_tskit_viz_other_graph>`. In particular, the Hudson "full ARG"
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model guarantees that the graph consists of nodes which mark a split into two child lineages
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("common ancestor" nodes) or nodes which mark a split into two parent lineages
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("recombination" nodes). Such ARGs can be visualized drawing edges as horizontal and vertical
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lines (the "ortho" style in the [tskit_arg_visualiser](https://github.com/kitchensjn/tskit_arg_visualizer)
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software):
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("recombination" nodes). Such ARGs can be visualized with edges drawn as horizontal and vertical
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lines (the "ortho" style in the
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[tskit_arg_visualiser](https://github.com/kitchensjn/tskit_arg_visualizer) software):
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```{code-cell} ipython3
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:"tags": ["hide-input"]
@@ -209,7 +209,7 @@ print(
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:::{note}
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This likelihood calculation is tied to the specific `tskit` representation of the ARG that
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is output by the `msprime` simulator. In particular, it expects each recombination event to
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correspond to two recombination nodes, which allows so-called `diamond` events to be
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correspond to two recombination nodes, which allows so-called "diamond" events to be
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represented, in which both parents at a recombination event trace directly back to the
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same common ancestor.
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:::
@@ -307,7 +307,12 @@ _recombination_, and _sampling_ events), with the genomic regions of inheritance
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encoded by storing a specific breakpoint location on each recombination node.
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In contrast, nodes in a `tskit` ARG correspond to _genomes_, and inherited regions
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are defined by intervals stored on *edges* (via the {attr}`~Edge.left` and
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{attr}`~Edge.right` properties), rather than on nodes.
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{attr}`~Edge.right` properties), rather than on nodes. Here, for example, is the
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edge table from our ARG:
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```{code-cell}
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ts_arg.tables.edges
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```
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Technically therefore, ARGs stored by `tskit` are edge-annotated
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"genome ARGs", or [gARGs](https://www.biorxiv.org/content/10.1101/2023.11.03.565466v1).

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