How To Install cd-hit on Kali Linux

Introduction

In this tutorial we learn how to install cd-hit on Kali Linux.

What is cd-hit

cd-hit is:

cd-hit contains a number of programs designed to quickly group sequences. cd-hit groups proteins into clusters that meet a user-defined similarity threshold. cd-hit-est is similar to cd-hit, but designed to group nucleotide sequences (without introns). cd-hit-est-2d is similar to cd-hit-2d but designed to compare two nucleotide datasets. A number of other related programs are also in this package. Please see the cd-hit user manual, also part of this package, for further information.

There are three methods to install cd-hit on Kali Linux. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install cd-hit Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install cd-hit

Install cd-hit Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install cd-hit

Install cd-hit Using aptitude

If you want to follow this method, you might need to install aptitude on Kali Linux first since aptitude is usually not installed by default on Kali Linux. Update apt database with aptitude using the following command.

sudo aptitude update

After updating apt database, We can install cd-hit using aptitude by running the following command:

sudo aptitude -y install cd-hit

How To Uninstall cd-hit on Kali Linux

To uninstall only the cd-hit package we can use the following command:

sudo apt-get remove cd-hit

Uninstall cd-hit And Its Dependencies

To uninstall cd-hit and its dependencies that are no longer needed by Kali Linux, we can use the command below:

sudo apt-get -y autoremove cd-hit

Remove cd-hit Configurations and Data

To remove cd-hit configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge cd-hit

Remove cd-hit configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge cd-hit

Dependencies

cd-hit have the following dependencies:

• libc6
• libgcc-s1
• libgomp1
• libstdc++6
• zlib1g

References

• cd-hit website

Summary

In this tutorial we learn how to install cd-hit package on Kali Linux using different package management tools: apt, apt-get and aptitude.