How To Install vienna-rna on Kali Linux
Introduction
In this tutorial we learn how to install vienna-rna
on Kali Linux.
What is vienna-rna
vienna-rna is:
The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. It is developed and maintained by the group of Ivo Hofacker in Vienna.
RNA secondary structure prediction through energy minimization is the most used function in the package. It provides three kinds of dynamic programming algorithms for structure prediction:
- the minimum free energy algorithm of (Zuker & Stiegler 1981) which yields a single optimal structure,
- the partition function algorithm of (McCaskill 1990) which calculates base pair probabilities in the thermodynamic ensemble, and the suboptimal folding algorithm of (Wuchty et.al 1999) which generates all suboptimal structures within a given energy range of the optimal energy.
For secondary structure comparison, the package contains several measures of distance (dissimilarities) using either string alignment or tree-editing (Shapiro & Zhang 1990). Finally, is provided an algorithm to design sequences with a predefined structure (inverse folding). The RNAforester package is a tool for aligning RNA secondary structures and it’s user interface integrates to those of the tools of the Vienna RNA package.
There are three methods to install vienna-rna
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 vienna-rna Using apt-get
Update apt database with apt-get
using the following command.
sudo apt-get update
After updating apt database, We can install vienna-rna
using apt-get
by running the following command:
sudo apt-get -y install vienna-rna
Install vienna-rna Using apt
Update apt database with apt
using the following command.
sudo apt update
After updating apt database, We can install vienna-rna
using apt
by running the following command:
sudo apt -y install vienna-rna
Install vienna-rna 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 vienna-rna
using aptitude
by running the following command:
sudo aptitude -y install vienna-rna
How To Uninstall vienna-rna on Kali Linux
To uninstall only the vienna-rna
package we can use the following command:
sudo apt-get remove vienna-rna
Uninstall vienna-rna And Its Dependencies
To uninstall vienna-rna
and its dependencies that are no longer needed by Kali Linux, we can use the command below:
sudo apt-get -y autoremove vienna-rna
Remove vienna-rna Configurations and Data
To remove vienna-rna
configuration and data from Kali Linux we can use the following command:
sudo apt-get -y purge vienna-rna
Remove vienna-rna configuration, data, and all of its dependencies
We can use the following command to remove vienna-rna
configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge vienna-rna
Dependencies
vienna-rna have the following dependencies:
References
Summary
In this tutorial we learn how to install vienna-rna
package on Kali Linux using different package management tools: apt
, apt-get
and aptitude
.