mafft command not found

In this troubleshooting guide we learn how to fix mafft command not found error message

Introduction

When you run more command in linux terminal / console, you get the following error message

mafft: command not found

or when using sudo you get the following error message

sudo: mafft: command not found

In Ubuntu mafft is provided by mafft package.

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).

To fix this problem, we can install more using the command below.

sudo apt-get -y install mafft

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install mafft.

sudo apt -y install mafft

Or if you have aptitude installed you can use the following command.

sudo aptitude install mafft

In this tutorial we learn how to fix mafft command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.