iterative_cdhit command not found

Introduction

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

iterative_cdhit: command not found

or when using sudo you get the following error message

sudo: iterative_cdhit: command not found

Solutions to iterative_cdhit: command not found

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

In Ubuntu iterative_cdhit is provided by roary package.

roary is:

Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (as produced, for instance, by Prokka) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, something which is computationally infeasible with existing methods, without compromising the quality of the results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a single processor. To perform this analysis using existing methods would take weeks and hundreds of GB of RAM. Roary is not intended for meta-genomics or for comparing extremely diverse sets of genomes.

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

sudo apt-get -y install roary

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

You can also use apt command to install roary.

sudo apt -y install roary

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

sudo aptitude install roary

Summary

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