How To Install mafft on Ubuntu

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

3 minutes  • 431 words

Introduction

In this tutorial we learn how to install mafft on Ubuntu.

What is mafft

mafft is:

MAFFT is a multiple sequence alignment program which offers three accuracy-oriented methods:

• L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information),
• G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information),
• E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences), and five speed-oriented methods:
• FFT-NS-i (iterative refinement method; two cycles only),
• FFT-NS-i (iterative refinement method; max. 1000 iterations),
• FFT-NS-2 (fast; progressive method),
• FFT-NS-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree),
• NW-NS-PartTree-1 (recommended for ∼50,000 sequences; progressive method with the PartTree algorithm).

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

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

sudo apt-get update

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

sudo apt-get -y install mafft

Install mafft Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install mafft

Install mafft 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 mafft using aptitude by running the following command:

sudo aptitude -y install mafft

How To Uninstall mafft on Ubuntu

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

sudo apt-get remove mafft

Uninstall mafft And Its Dependencies

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

sudo apt-get -y autoremove mafft

Remove mafft Configurations and Data

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

sudo apt-get -y purge mafft

Remove mafft configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge mafft

Dependencies

mafft have the following dependencies:

• libc6
• perl

References

• mafft website

Summary

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