How To Install hyphy-pt on Kali Linux

In this tutorial we learn how to install hyphy-pt on Kali Linux. hyphy-pt is Hypothesis testing using Phylogenies (pthreads version)

Introduction

In this tutorial we learn how to install hyphy-pt on Kali Linux.

What is hyphy-pt

hyphy-pt is:

HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for parallel computing environments (via message passing interface) and it can be compiled as a shared library and called from other programming environments such as Python or R. Continued development of HyPhy is currently supported in part by an NIGMS R01 award 1R01GM093939.

This package provides an executable using pthreads to do multiprocessing.

There are three methods to install hyphy-pt 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 hyphy-pt Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install hyphy-pt

Install hyphy-pt Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install hyphy-pt

Install hyphy-pt 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 hyphy-pt using aptitude by running the following command:

sudo aptitude -y install hyphy-pt

How To Uninstall hyphy-pt on Kali Linux

To uninstall only the hyphy-pt package we can use the following command:

sudo apt-get remove hyphy-pt

Uninstall hyphy-pt And Its Dependencies

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

sudo apt-get -y autoremove hyphy-pt

Remove hyphy-pt Configurations and Data

To remove hyphy-pt configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge hyphy-pt

Remove hyphy-pt configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge hyphy-pt

Dependencies

hyphy-pt have the following dependencies:

References

Summary

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