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    "# Display a Phylogenetic Tree with a Square Dendrogram Style\n",
    "\n",
    "We use a tree saved in `json` format from a likelihood function analysis of a non-stationary model. The tree was derived such that the the branch lengths are now \"ENS\"."
   ]
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       "                        {\"responsive\": true}\n",
       "                    ).then(function(){\n",
       "                            \n",
       "var gd = document.getElementById('b99d7eb6-ee52-41db-8016-75aba7bceb91');\n",
       "var x = new MutationObserver(function (mutations, observer) {{\n",
       "        var display = window.getComputedStyle(gd).display;\n",
       "        if (!display || display === 'none') {{\n",
       "            console.log([gd, 'removed!']);\n",
       "            Plotly.purge(gd);\n",
       "            observer.disconnect();\n",
       "        }}\n",
       "}});\n",
       "\n",
       "// Listen for the removal of the full notebook cells\n",
       "var notebookContainer = gd.closest('#notebook-container');\n",
       "if (notebookContainer) {{\n",
       "    x.observe(notebookContainer, {childList: true});\n",
       "}}\n",
       "\n",
       "// Listen for the clearing of the current output cell\n",
       "var outputEl = gd.closest('.output');\n",
       "if (outputEl) {{\n",
       "    x.observe(outputEl, {childList: true});\n",
       "}}\n",
       "\n",
       "                        })\n",
       "                };\n",
       "                });\n",
       "            </script>\n",
       "        </div>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "from cogent3.app import io\n",
    "\n",
    "reader = io.load_json()\n",
    "\n",
    "ens_tree = reader(\"../data/GN-tree.json\")\n",
    "fig = ens_tree.get_figure(width=600, height=600)\n",
    "fig.show()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Changing scale bar placement"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "        if (typeof require !== 'undefined') {\n",
       "        require.undef(\"plotly\");\n",
       "        requirejs.config({\n",
       "            paths: {\n",
       "                'plotly': ['https://cdn.plot.ly/plotly-latest.min']\n",
       "            }\n",
       "        });\n",
       "        require(['plotly'], function(Plotly) {\n",
       "            window._Plotly = Plotly;\n",
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       "        }\n",
       "        </script>\n",
       "        "
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    "fig.scale_bar = \"top right\"\n",
    "fig.show()"
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  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Colouring a set of edges"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
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       "            console.log([gd, 'removed!']);\n",
       "            Plotly.purge(gd);\n",
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       "}});\n",
       "\n",
       "// Listen for the removal of the full notebook cells\n",
       "var notebookContainer = gd.closest('#notebook-container');\n",
       "if (notebookContainer) {{\n",
       "    x.observe(notebookContainer, {childList: true});\n",
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       "var outputEl = gd.closest('.output');\n",
       "if (outputEl) {{\n",
       "    x.observe(outputEl, {childList: true});\n",
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       "            </script>\n",
       "        </div>"
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     "metadata": {},
     "output_type": "display_data"
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   ],
   "source": [
    "fig.style_edges(\"AfricanEl\", tip2=\"Manatee\", legendgroup=\"Afrotheria\", \n",
    "                line=dict(color=\"magenta\"))\n",
    "fig.show()"
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  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## With Contemporaneous Tips"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
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