How To Install physamp on Kali Linux

In this tutorial we learn how to install physamp on Kali Linux. physamp is sample sequence alignment corresponding to phylogeny

Introduction

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

What is physamp

physamp is:

The PhySamp package currently contains two programs: bppphysamp, which samples sequences according to their similarity, and bppalnoptim, which samples a sequence alignment by removing sequences in order to maximize the number of sites suitable for a given analysis. The bppalnoptim program has three running modes:

  • Interactive: the user will be iteratively proposed a set of choices for sequence removal, with their corresponding site gains. The procedure stops when the user does not want to remove more sequences, and the resulting filtered alignment is written.
  • Automatic: the user enters an a priori criterion for stopping the filtering procedure (for instance a minimum number of sequences to keep).
  • Diagnostic: this mode allows one to plot the trade-off curve, by showing the site gain as a function of the number of removed sequences.

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

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

sudo apt-get update

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

sudo apt-get -y install physamp

Install physamp Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install physamp

Install physamp 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 physamp using aptitude by running the following command:

sudo aptitude -y install physamp

How To Uninstall physamp on Kali Linux

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

sudo apt-get remove physamp

Uninstall physamp And Its Dependencies

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

sudo apt-get -y autoremove physamp

Remove physamp Configurations and Data

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

sudo apt-get -y purge physamp

Remove physamp configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge physamp

Dependencies

physamp have the following dependencies:

References

Summary

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