How To Install jaligner on Ubuntu 22.04

In this tutorial we learn how to install jaligner on Ubuntu 22.04. jaligner is Smith-Waterman algorithm with Gotohs improvement

Introduction

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

What is jaligner

jaligner is:

JAligner is an open source Java implementation of the Smith-Waterman algorithm with Gotoh’s improvement for biological local pairwise sequence alignment with the affine gap penalty model.

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

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

sudo apt-get update

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

sudo apt-get -y install jaligner

Install jaligner Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install jaligner

Install jaligner 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 jaligner using aptitude by running the following command:

sudo aptitude -y install jaligner

How To Uninstall jaligner on Ubuntu 22.04

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

sudo apt-get remove jaligner

Uninstall jaligner And Its Dependencies

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

sudo apt-get -y autoremove jaligner

Remove jaligner Configurations and Data

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

sudo apt-get -y purge jaligner

Remove jaligner configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge jaligner

References

Summary

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