How To Install physamp on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 459 words
Introduction
In this tutorial we learn how to install physamp on Ubuntu.
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 Ubuntu. 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 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 physamp using aptitude by running the following command:
sudo aptitude -y install physamp
How To Uninstall physamp on Ubuntu
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 Ubuntu, we can use the command below:
sudo apt-get -y autoremove physamp
Remove physamp Configurations and Data
To remove physamp configuration and data from Ubuntu 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 Ubuntu using different package management tools: apt, apt-get and aptitude.