How To Install cd-hit on Ubuntu 18.04
Introduction
In this tutorial we learn how to install cd-hit on Ubuntu 18.04.
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 Ubuntu 18.04. 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 first since aptitude is usually not installed by default on Ubuntu. 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 Ubuntu 18.04
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 Ubuntu 18.04, 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 Ubuntu 18.04 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
References
Summary
In this tutorial we learn how to install cd-hit package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
