treetime command not found

In this troubleshooting guide we learn how to fix treetime command not found error message

Introduction

When you run more command in linux terminal / console, you get the following error message

treetime: command not found

or when using sudo you get the following error message

sudo: treetime: command not found

Solutions to treetime: command not found

How To Fix treetime: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu treetime is provided by python3-treetime package.

python3-treetime is:

TreeTime provides routines for ancestral sequence reconstruction and the maximum likelihoo inference of molecular-clock phylogenies, i.e., a tree where all branches are scaled such that the locations of terminal nodes correspond to their sampling times and internal nodes are placed at the most likely time of divergence.

TreeTime aims at striking a compromise between sophisticated probabilistic models of evolution and fast heuristics. It implements GTR models of ancestral inference and branch length optimization, but takes the tree topology as given. To optimize the likelihood of time-scaled phylogenies, treetime uses an iterative approach that first infers ancestral sequences given the branch length of the tree, then optimizes the positions of unconstraine d nodes on the time axis, and then repeats this cycle. The only topology optimization are (optional) resolution of polytomies in a way that is most (approximately) consistent with the sampling time constraints on the tree. The package is designed to be used as a stand-alone tool or as a library used in larger phylogenetic analysis workflows.

Features

  • ancestral sequence reconstruction (marginal and joint maximum likelihood)
  • molecular clock tree inference (marginal and joint maximum likelihood)
  • inference of GTR models
  • rerooting to obtain best root-to-tip regression
  • auto-correlated relaxed molecular clock (with normal prior)

This package provides the Python 3 module.

To fix this problem, we can install more using the command below.

sudo apt-get -y install python3-treetime

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install python3-treetime.

sudo apt -y install python3-treetime

Or if you have aptitude installed you can use the following command.

sudo aptitude install python3-treetime

Summary

In this tutorial we learn how to fix treetime command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.