maf-cut command not found

In this troubleshooting guide we learn how to fix maf-cut command not found error message

Introduction

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

maf-cut: command not found

or when using sudo you get the following error message

sudo: maf-cut: command not found

Solutions to maf-cut: command not found

How To Fix maf-cut: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu maf-cut is provided by last-align package.

last-align is:

LAST is software for comparing and aligning sequences, typically DNA or protein sequences. LAST is similar to BLAST, but it copes better with very large amounts of sequence data. Here are two things LAST is good at:

Comparing large (e.g. mammalian) genomes.
Mapping lots of sequence tags onto a genome.

The main technical innovation is that LAST finds initial matches based on their multiplicity, instead of using a fixed size (e.g. BLAST uses 10-mers). This allows one to map tags to genomes without repeat-masking, without becoming overwhelmed by repetitive hits. To find these variable-sized matches, it uses a suffix array (inspired by Vmatch). To achieve high sensitivity, it uses a discontiguous suffix array, analogous to spaced seeds.

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

sudo apt-get -y install last-align

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

You can also use apt command to install last-align.

sudo apt -y install last-align

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

sudo aptitude install last-align

Summary

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