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phylogram_visualization

Create a family-level phylogram based on the Dated angiosperm phylogram file provided in (https://bdj.pensoft.net/article/39677/instance/5312825/ Suppl. material 5) using ETE Toolkit

Manual preparations: The source phylogram is provided in a format that is not readable by ETE Toolkit. The following steps were needed to convert it to a readable Newick format:

  • Extract the actual tree: $ awk '/^tree /' oo_330891.tre > largetree.tre
  • Manually remove the leading and closing elements that do not belong to Newick format
  • remove additional node attributes: $ sed "s/[[][^]]*[]]//g" largetree.tre > largetree_pruned.tre
  • Replace numerical leaf names with correpsonding species name, as listed in the TRANSLATE section of the original file (best done programmatically)

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