How To Install edlib-aligner on Ubuntu

Posted on April 1, 2023 (Last modified on May 20, 2023 )

3 minutes • 465 words

Introduction

In this tutorial we learn how to install edlib-aligner on Ubuntu.

What is `edlib-aligner`

edlib-aligner is:

Edlib is a lightweight and super fast C/C++ library for sequence alignment using edit distance. This package provides an aligner using this library.

Features of libedlib

Calculates edit distance (Levehnstein distance).
It can find optimal alignment path (instructions how to transform first sequence into the second sequence).
It can find just the start and/or end locations of alignment path - can be useful when speed is more important than having exact alignment path.
Supports multiple alignment methods: global(NW), prefix(SHW) and infix(HW), each of them useful for different scenarios.
You can extend character equality definition, enabling you to e.g. have wildcard characters, to have case insensitive alignment or to work with degenerate nucleotides.
It can easily handle small or very large sequences, even when finding alignment path, while consuming very little memory.
Super fast thanks to Myers’s bit-vector algorithm.

There are three methods to install edlib-aligner on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install edlib-aligner Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install edlib-aligner

Install edlib-aligner Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install edlib-aligner

Install edlib-aligner 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 edlib-aligner using aptitude by running the following command:

sudo aptitude -y install edlib-aligner

How To Uninstall edlib-aligner on Ubuntu

To uninstall only the edlib-aligner package we can use the following command:

sudo apt-get remove edlib-aligner

Uninstall edlib-aligner And Its Dependencies

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

sudo apt-get -y autoremove edlib-aligner

Remove edlib-aligner Configurations and Data

To remove edlib-aligner configuration and data from Ubuntu we can use the following command:

sudo apt-get -y purge edlib-aligner

Remove edlib-aligner configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge edlib-aligner

Dependencies

edlib-aligner have the following dependencies:

References

edlib-aligner website

Summary

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