Introduction
In this tutorial we learn how to install beast2-mcmc on Ubuntu 22.04.
What is beast2-mcmc
beast2-mcmc is:
BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
sequences. It is entirely orientated towards rooted, time-measured
phylogenies inferred using strict or relaxed molecular clock models. It
can be used as a method of reconstructing phylogenies but is also a
framework for testing evolutionary hypotheses without conditioning on a
single tree topology. BEAST uses MCMC to average over tree space, so that
each tree is weighted proportional to its posterior probability. Included
is a simple to use user-interface program for setting up standard
analyses and a suit of programs for analysing the results.
This is no new upstream version of beast-mcmc (1.x) but rather a rewritten
version.
There are three methods to install beast2-mcmc on Ubuntu 22.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install beast2-mcmc Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install beast2-mcmc using apt-get by running the following command:
sudo apt-get -y install beast2-mcmc
Install beast2-mcmc Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install beast2-mcmc using apt by running the following command:
sudo apt -y install beast2-mcmc
Install beast2-mcmc Using aptitude
If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install beast2-mcmc using aptitude by running the following command:
sudo aptitude -y install beast2-mcmc
How To Uninstall beast2-mcmc on Ubuntu 22.04
To uninstall only the beast2-mcmc package we can use the following command:
sudo apt-get remove beast2-mcmc
Uninstall beast2-mcmc And Its Dependencies
To uninstall beast2-mcmc and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove beast2-mcmc
Remove beast2-mcmc Configurations and Data
To remove beast2-mcmc configuration and data from Ubuntu 22.04 we can use the following command:
sudo apt-get -y purge beast2-mcmc
Remove beast2-mcmc configuration, data, and all of its dependencies
We can use the following command to remove beast2-mcmc configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge beast2-mcmc
References
Summary
In this tutorial we learn how to install beast2-mcmc package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.
