How To Install python-freecontact on Ubuntu 18.04
Introduction
In this tutorial we learn how to install python-freecontact on Ubuntu 18.04.
What is python-freecontact
python-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 Python binding.
There are three methods to install python-freecontact 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 python-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 python-freecontact using apt-get by running the following command:
sudo apt-get -y install python-freecontact
Install python-freecontact Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install python-freecontact using apt by running the following command:
sudo apt -y install python-freecontact
Install python-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 Ubuntu. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install python-freecontact using aptitude by running the following command:
sudo aptitude -y install python-freecontact
How To Uninstall python-freecontact on Ubuntu 18.04
To uninstall only the python-freecontact package we can use the following command:
sudo apt-get remove python-freecontact
Uninstall python-freecontact And Its Dependencies
To uninstall python-freecontact and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove python-freecontact
Remove python-freecontact Configurations and Data
To remove python-freecontact configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge python-freecontact
Remove python-freecontact configuration, data, and all of its dependencies
We can use the following command to remove python-freecontact configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge python-freecontact
References
Summary
In this tutorial we learn how to install python-freecontact package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
