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)