How To Install python3-treetime on Kali Linux
Introduction
In this tutorial we learn how to install python3-treetime on Kali Linux.
What is python3-treetime
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.
There are three methods to install python3-treetime on Kali Linux. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install python3-treetime Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get updateAfter updating apt database, We can install python3-treetime using apt-get by running the following command:
sudo apt-get -y install python3-treetimeInstall python3-treetime Using apt
Update apt database with apt using the following command.
sudo apt updateAfter updating apt database, We can install python3-treetime using apt by running the following command:
sudo apt -y install python3-treetimeInstall python3-treetime Using aptitude
If you want to follow this method, you might need to install aptitude on Kali Linux first since aptitude is usually not installed by default on Kali Linux. Update apt database with aptitude using the following command.
sudo aptitude updateAfter updating apt database, We can install python3-treetime using aptitude by running the following command:
sudo aptitude -y install python3-treetimeHow To Uninstall python3-treetime on Kali Linux
To uninstall only the python3-treetime package we can use the following command:
sudo apt-get remove python3-treetimeUninstall python3-treetime And Its Dependencies
To uninstall python3-treetime and its dependencies that are no longer needed by Kali Linux, we can use the command below:
sudo apt-get -y autoremove python3-treetimeRemove python3-treetime Configurations and Data
To remove python3-treetime configuration and data from Kali Linux we can use the following command:
sudo apt-get -y purge python3-treetimeRemove python3-treetime configuration, data, and all of its dependencies
We can use the following command to remove python3-treetime configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge python3-treetimeDependencies
python3-treetime have the following dependencies:
References
Summary
In this tutorial we learn how to install python3-treetime package on Kali Linux using different package management tools: apt, apt-get and aptitude.
