How To Install t-coffee on Debian 9
Introduction
In this tutorial we learn how to install t-coffee on Debian 9.
What is t-coffee
t-coffee is:
T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can mix sequences and structures.
T-Coffee allows the combination of a collection of multiple/pairwise, global or local alignments into a single model. It can also estimate the level of consistency of each position within the new alignment with the rest of the alignments. See the pre-print for more information
T-Coffee has a special called M-Coffee that makes it possible to combine the output of many multiple sequence alignment packages. In its published version, it uses MUSCLE, PROBCONS, POA, DiAlign-TS, MAFFT, Clustal?W, PCMA and T-Coffee. A special version has been made for Debian, DM-Coffee, that uses only free software by replacing Clustal?W by Kalign. Using the 8 Methods of M-Coffee can sometimes be a bit heavy. You can use a subset of your favorite methods if you prefer.
There are three methods to install t-coffee on Debian 9. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install t-coffee Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install t-coffee using apt-get by running the following command:
sudo apt-get -y install t-coffee
Install t-coffee Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install t-coffee using apt by running the following command:
sudo apt -y install t-coffee
Install t-coffee 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 Debian. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install t-coffee using aptitude by running the following command:
sudo aptitude -y install t-coffee
How To Uninstall t-coffee on Debian 9
To uninstall only the t-coffee package we can use the following command:
sudo apt-get remove t-coffee
Uninstall t-coffee And Its Dependencies
To uninstall t-coffee and its dependencies that are no longer needed by Debian 9, we can use the command below:
sudo apt-get -y autoremove t-coffee
Remove t-coffee Configurations and Data
To remove t-coffee configuration and data from Debian 9 we can use the following command:
sudo apt-get -y purge t-coffee
Remove t-coffee configuration, data, and all of its dependencies
We can use the following command to remove t-coffee configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge t-coffee
Dependencies
t-coffee have the following dependencies:
References
Summary
In this tutorial we learn how to install t-coffee package on Debian 9 using different package management tools: apt, apt-get and aptitude.