How To Install pal2nal on Kali Linux

Introduction

In this tutorial we learn how to install pal2nal on Kali Linux.

What is pal2nal

pal2nal is:

PAL2NAL is a program that converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon-based DNA alignment. The program automatically assigns the corresponding codon sequence even if the input DNA sequence has mismatches with the input protein sequence, or contains UTRs, polyA tails. It can also deal with frame shifts in the input alignment, which is suitable for the analysis of pseudogenes. The resulting codon-based DNA alignment can further be subjected to the calculation of synonymous (Ks) and non-synonymous (Ka) substitution rates.

There are three methods to install pal2nal 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 pal2nal Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install pal2nal using apt-get by running the following command:

sudo apt-get -y install pal2nal

Install pal2nal Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install pal2nal using apt by running the following command:

sudo apt -y install pal2nal

Install pal2nal 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 pal2nal using aptitude by running the following command:

sudo aptitude -y install pal2nal

How To Uninstall pal2nal on Kali Linux

To uninstall only the pal2nal package we can use the following command:

sudo apt-get remove pal2nal

Uninstall pal2nal And Its Dependencies

To uninstall pal2nal and its dependencies that are no longer needed by Kali Linux, we can use the command below:

sudo apt-get -y autoremove pal2nal

Remove pal2nal Configurations and Data

To remove pal2nal configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge pal2nal

Remove pal2nal configuration, data, and all of its dependencies

We can use the following command to remove pal2nal configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge pal2nal

Dependencies

pal2nal have the following dependencies:

References

• pal2nal website

Summary

In this tutorial we learn how to install pal2nal package on Kali Linux using different package management tools: apt, apt-get and aptitude.