How To Install freecontact on Debian 9
Introduction
In this tutorial we learn how to install freecontact on Debian 9.
What is freecontact
freecontact is:
FreeContact is a protein residue contact predictor optimized for speed. Its input is a multiple sequence alignment. FreeContact can function as an accelerated drop-in for the published contact predictors EVfold-mfDCA of DS. Marks (2011) and PSICOV of D. Jones (2011).
FreeContact is accelerated by a combination of vector instructions, multiple threads, and faster implementation of key parts. Depending on the alignment, 8-fold or higher speedups are possible.
A sufficiently large alignment is required for meaningful results. As a minimum, an alignment with an effective (after-weighting) sequence count bigger than the length of the query sequence should be used. Alignments with tens of thousands of (effective) sequences are considered good input.
jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite can be used to generate the alignments, for example.
This package contains the command line tool freecontact(1).
There are three methods to install freecontact 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 freecontact Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install freecontact using apt-get by running the following command:
sudo apt-get -y install freecontact
Install freecontact Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install freecontact using apt by running the following command:
sudo apt -y install freecontact
Install freecontact 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 freecontact using aptitude by running the following command:
sudo aptitude -y install freecontact
How To Uninstall freecontact on Debian 9
To uninstall only the freecontact package we can use the following command:
sudo apt-get remove freecontact
Uninstall freecontact And Its Dependencies
To uninstall freecontact and its dependencies that are no longer needed by Debian 9, we can use the command below:
sudo apt-get -y autoremove freecontact
Remove freecontact Configurations and Data
To remove freecontact configuration and data from Debian 9 we can use the following command:
sudo apt-get -y purge freecontact
Remove freecontact configuration, data, and all of its dependencies
We can use the following command to remove freecontact configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge freecontact
Dependencies
freecontact have the following dependencies:
References
Summary
In this tutorial we learn how to install freecontact package on Debian 9 using different package management tools: apt, apt-get and aptitude.