@@ -99,9 +99,9 @@ trees. However, all tree sequences can also be
9999{ref}` plotted as graphs<sec_tskit_viz_other_graph> ` . In particular, the Hudson "full ARG"
100100model guarantees that the graph consists of nodes which mark a split into two child lineages
101101("common ancestor" nodes) or nodes which mark a split into two parent lineages
102- ("recombination" nodes). Such ARGs can be visualized drawing edges as horizontal and vertical
103- lines (the "ortho" style in the [ tskit_arg_visualiser ] ( https://github.com/kitchensjn/tskit_arg_visualizer )
104- software):
102+ ("recombination" nodes). Such ARGs can be visualized with edges drawn as horizontal and vertical
103+ lines (the "ortho" style in the
104+ [ tskit_arg_visualiser ] ( https://github.com/kitchensjn/tskit_arg_visualizer ) software):
105105
106106``` {code-cell} ipython3
107107:"tags": ["hide-input"]
@@ -209,7 +209,7 @@ print(
209209:::{note}
210210This likelihood calculation is tied to the specific ` tskit ` representation of the ARG that
211211is output by the ` msprime ` simulator. In particular, it expects each recombination event to
212- correspond to two recombination nodes, which allows so-called ` diamond ` events to be
212+ correspond to two recombination nodes, which allows so-called " diamond" events to be
213213represented, in which both parents at a recombination event trace directly back to the
214214same common ancestor.
215215:::
@@ -307,7 +307,12 @@ _recombination_, and _sampling_ events), with the genomic regions of inheritance
307307encoded by storing a specific breakpoint location on each recombination node.
308308In contrast, nodes in a ` tskit ` ARG correspond to _ genomes_ , and inherited regions
309309are defined by intervals stored on * edges* (via the {attr}` ~Edge.left ` and
310- {attr}` ~Edge.right ` properties), rather than on nodes.
310+ {attr}` ~Edge.right ` properties), rather than on nodes. Here, for example, is the
311+ edge table from our ARG:
312+
313+ ``` {code-cell}
314+ ts_arg.tables.edges
315+ ```
311316
312317Technically therefore, ARGs stored by ` tskit ` are edge-annotated
313318"genome ARGs", or [ gARGs] ( https://www.biorxiv.org/content/10.1101/2023.11.03.565466v1 ) .
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