How To Install beast2-mcmc on Ubuntu 20.04

In this tutorial we learn how to install beast2-mcmc on Ubuntu 20.04. beast2-mcmc is Bayesian MCMC phylogenetic inference

Introduction

In this tutorial we learn how to install beast2-mcmc on Ubuntu 20.04.

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 20.04. 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 20.04

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 20.04, 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 20.04 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 20.04 using different package management tools: apt, apt-get and aptitude.