How To Install pplacer on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
2 minutes • 394 words
Introduction
In this tutorial we learn how to install pplacer on Ubuntu.
What is pplacer
pplacer is:
Pplacer places reads on a phylogenetic tree. guppy (Grand Unified Phylogenetic Placement Yanalyzer) yanalyzes them. rppr is a helpful tool for working with reference packages.
Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.
There are three methods to install pplacer 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 pplacer Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install pplacer using apt-get by running the following command:
sudo apt-get -y install pplacer
Install pplacer Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install pplacer using apt by running the following command:
sudo apt -y install pplacer
Install pplacer 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 pplacer using aptitude by running the following command:
sudo aptitude -y install pplacer
How To Uninstall pplacer on Ubuntu
To uninstall only the pplacer package we can use the following command:
sudo apt-get remove pplacer
Uninstall pplacer And Its Dependencies
To uninstall pplacer and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove pplacer
Remove pplacer Configurations and Data
To remove pplacer configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge pplacer
Remove pplacer configuration, data, and all of its dependencies
We can use the following command to remove pplacer configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge pplacer
Dependencies
pplacer have the following dependencies:
References
Summary
In this tutorial we learn how to install pplacer package on Ubuntu using different package management tools: apt, apt-get and aptitude.