General requirements to run any of the python scripts are in requirements.txt
auc.py
Calculate AUC for precision-recall and receiver operating characteristic curves
for tree topology support estimates.
concat.py
Concatenate multiple sequence alignments for use in other analyses (e.g. RAxML concatenated).
pairwise-nrf.py
Calculate the mean robinson-foulds distance between each pair of trees given as input.
scaletree.py
Scale branch-lengths either by a constant factor or to achieve a desired tree height
(maximum root-to-tip distance). Can also introduce ultrametricity by the procedure
described in Moret et al., 2002