How To Install phyx on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 446 words
Introduction
In this tutorial we learn how to install phyx on Ubuntu.
What is phyx
phyx is:
phyx provides a convenient, lightweight and inclusive toolkit consisting of programs spanning the wide breadth of programs utilized by researchers performing phylogenomic analyses. Modeled after Unix/GNU/Linux command line tools, individual programs perform a single task and operate on standard I/O streams. A result of this stream-centric approach is that, for most programs, only a single sequence or tree is in memory at any moment. Thus, large datasets can be processed with minimal memory requirements. phyx’s ever-growing complement of programs consists of over 35 programs focused on exploring, manipulating, analyzing and simulating phylogenetic objects (alignments, trees and MCMC logs). As with standard Unix command line tools, these programs can be piped (together with non-phyx tools), allowing the easy construction of efficient analytical pipelines.
There are three methods to install phyx 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 phyx Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install phyx using apt-get by running the following command:
sudo apt-get -y install phyx
Install phyx Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install phyx using apt by running the following command:
sudo apt -y install phyx
Install phyx 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 phyx using aptitude by running the following command:
sudo aptitude -y install phyx
How To Uninstall phyx on Ubuntu
To uninstall only the phyx package we can use the following command:
sudo apt-get remove phyx
Uninstall phyx And Its Dependencies
To uninstall phyx and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove phyx
Remove phyx Configurations and Data
To remove phyx configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge phyx
Remove phyx configuration, data, and all of its dependencies
We can use the following command to remove phyx configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge phyx
Dependencies
phyx have the following dependencies:
References
Summary
In this tutorial we learn how to install phyx package on Ubuntu using different package management tools: apt, apt-get and aptitude.