treetime

TreeTime provides routines for ancestral sequence reconstruction and inference of molecular-clock phylogenies. More information: <https://treetime.readthedocs.io/en/latest/tutorials.html>.

Install

All systems
curl cmd.cat/treetime.sh
Debian Debian
apt-get install python3-treetime
Ubuntu
apt-get install python3-treetime
image/svg+xml Kali Linux
apt-get install python3-treetime
Windows (WSL2)
sudo apt-get update sudo apt-get install python3-treetime
Dockerfile
dockerfile.run/treetime

TreeTime provides routines for ancestral sequence reconstruction and inference of molecular-clock phylogenies. More information: <https://treetime.readthedocs.io/en/latest/tutorials.html>.

  • Infer ancestral sequences maximizing the joint or marginal likelihood:
    treetime ancestral
  • Analyze patterns of recurrent mutations aka homoplasies:
    treetime homoplasy
  • Estimate molecular clock parameters and reroot the tree:
    treetime clock
  • Map discrete character such as host or country to the tree:
    treetime mugration

© tl;dr; authors and contributors