How To Install prottest on Ubuntu 22.04
Introduction
In this tutorial we learn how to install prottest on Ubuntu 22.04.
What is prottest
prottest is:
PROTTEST (ModelTest’s relative) is a program for selecting the model of protein evolution that best fits a given set of sequences (alignment). This java program is based on the Phyml program (for maximum likelihood calculations and optimization of parameters) and uses the PAL library as well. Models included are empirical substitution matrices (such as WAG, LG, mtREV, Dayhoff, DCMut, JTT, VT, Blosum62, CpREV, RtREV, MtMam, MtArt, HIVb, and HIVw) that indicate relative rates of amino acid replacement, and specific improvements (+I:invariable sites, +G: rate heterogeneity among sites, +F: observed amino acid frequencies) to account for the evolutionary constraints impossed by conservation of protein structure and function. ProtTest uses the Akaike Information Criterion (AIC) and other statistics (AICc and BIC) to find which of the candidate models best fits the data at hand.
There are three methods to install prottest 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 prottest Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install prottest using apt-get by running the following command:
sudo apt-get -y install prottest
Install prottest Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install prottest using apt by running the following command:
sudo apt -y install prottest
Install prottest 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 prottest using aptitude by running the following command:
sudo aptitude -y install prottest
How To Uninstall prottest on Ubuntu 22.04
To uninstall only the prottest package we can use the following command:
sudo apt-get remove prottest
Uninstall prottest And Its Dependencies
To uninstall prottest and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove prottest
Remove prottest Configurations and Data
To remove prottest configuration and data from Ubuntu 22.04 we can use the following command:
sudo apt-get -y purge prottest
Remove prottest configuration, data, and all of its dependencies
We can use the following command to remove prottest configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge prottest
References
Summary
In this tutorial we learn how to install prottest package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.
