Changes tiplabels of a tree from TAG notation to individual names. This script can be run as follows:
change_tiplabels.R input_tree output_tree tag_indiv_df
where input_tree corresponds to the filename of the tree with TAG notation; output_tree to the tree with individual notation; tag_indiv_df the filename of a table that links TAGs to their individual names.
Short explanation on how to install and run ete3 on a server (without virtual display).
Visualization of phylogenetic trees used here in this thesis with ggtree and ape.
A script from Sidonie Bellot with minor changes. This scripts visualizes quartet support percentages (ASTRAL output) as pie charts on an ASTRAL tree.
Using the ape root() function for rooting a tree with the "edgelabel = TRUE" option, to assign the right support value to the right branch. However, due to the ASTRAL format, some formatting was needed with sed. The script can be run as follows:
root_tree.R input_tree output_tree outgroup
where input_tree is the ASTRAL tree (in newick format) that has to be rooted; output_tree is the name of the output tree and outgroup is the name of the outgroup (!has to be in the input_tree!).