How To Install physamp on Ubuntu 22.04
Introduction
In this tutorial we learn how to install physamp
on Ubuntu 22.04.
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 22.04. 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 22.04
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 22.04, 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 22.04 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
References
Summary
In this tutorial we learn how to install physamp
package on Ubuntu 22.04 using different package management tools: apt
, apt-get
and aptitude
.