cmscan command not found

Introduction

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

cmscan: command not found

or when using sudo you get the following error message

sudo: cmscan: command not found

Solutions to cmscan: command not found

How To Fix cmscan: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu cmscan is provided by infernal package.

infernal is:

Infernal (“INFERence of RNA ALignment”) searches DNA sequence databases for RNA structure and sequence similarities. It provides an implementation of a special variant of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.

The tool is an integral component of the Rfam database.

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

sudo apt-get -y install infernal

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

You can also use apt command to install infernal.

sudo apt -y install infernal

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

sudo aptitude install infernal

Summary

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