How To Install clonalframe on Ubuntu 22.04

In this tutorial we learn how to install clonalframe on Ubuntu 22.04. clonalframe is inference of bacterial microevolution using multilocus sequence data

Introduction

In this tutorial we learn how to install clonalframe on Ubuntu 22.04.

What is clonalframe

clonalframe is:

ClonalFrame identifies the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance.

ClonalFrame can be applied to any kind of sequence data, from a single fragment of DNA to whole genomes. It is well suited for the analysis of MLST data, where 7 gene fragments have been sequenced, but becomes progressively more powerful as the sequenced regions increase in length and number up to whole genomes. However, it requires the sequences to be aligned. If you have genomic data that is not aligned, it is recommend to use Mauve which produces alignment of whole bacterial genomes in exactly the format required for analysis with ClonalFrame.

There are three methods to install clonalframe 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 clonalframe Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install clonalframe using apt-get by running the following command:

sudo apt-get -y install clonalframe

Install clonalframe Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install clonalframe using apt by running the following command:

sudo apt -y install clonalframe

Install clonalframe 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 clonalframe using aptitude by running the following command:

sudo aptitude -y install clonalframe

How To Uninstall clonalframe on Ubuntu 22.04

To uninstall only the clonalframe package we can use the following command:

sudo apt-get remove clonalframe

Uninstall clonalframe And Its Dependencies

To uninstall clonalframe and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:

sudo apt-get -y autoremove clonalframe

Remove clonalframe Configurations and Data

To remove clonalframe configuration and data from Ubuntu 22.04 we can use the following command:

sudo apt-get -y purge clonalframe

Remove clonalframe configuration, data, and all of its dependencies

We can use the following command to remove clonalframe configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge clonalframe

References

Summary

In this tutorial we learn how to install clonalframe package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.