How To Install muscle on Debian 12
Introduction
In this tutorial we learn how to install muscle on Debian 12.
What is muscle
muscle is:
MUSCLE is a multiple alignment program for protein sequences. MUSCLE stands for multiple sequence comparison by log-expectation. In the authors tests, MUSCLE achieved the highest scores of all tested programs on several alignment accuracy benchmarks, and is also one of the fastest programs out there.
Muscle v5 is a major re-write of MUSCLE based on new algorithms.
Users should be aware that command line arguments compared to version 3.x of MUSCLE have changed!
Highest accuracy, scalable to thousands of sequences
Compared to previous versions, Muscle v5 is much more accurate, is often faster, and scales to much larger datasets. At the time of writing (late 2021), Muscle v5 has the highest scores on multiple alignment benchmarks including Balibase, Bralibase, Prefab and Balifam. It can align tens of thousands of sequences with high accuracy on a low-cost commodity computer (say, an 8-core Intel CPU with 32 Gb RAM). On large datasets, Muscle v5 is 20-30% more accurate than MAFFT and Clustal-Omega.
Alignment ensembles
Muscle v5 can generate ensembles of high-accuracy alternative alignments. All replicates have equal average accuracy on benchmark test, including the MSA made with default parameters. By comparing results of downstream analysis (trees, structure prediction…) on different replicates, you can assess the effects of alignment errors on your study.
There are three methods to install muscle on Debian 12. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install muscle Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install muscle using apt-get by running the following command:
sudo apt-get -y install muscle
Install muscle Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install muscle using apt by running the following command:
sudo apt -y install muscle
Install muscle 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 Debian. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install muscle using aptitude by running the following command:
sudo aptitude -y install muscle
How To Uninstall muscle on Debian 12
To uninstall only the muscle package we can use the following command:
sudo apt-get remove muscle
Uninstall muscle And Its Dependencies
To uninstall muscle and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove muscle
Remove muscle Configurations and Data
To remove muscle configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge muscle
Remove muscle configuration, data, and all of its dependencies
We can use the following command to remove muscle configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge muscle
Dependencies
muscle have the following dependencies:
References
Summary
In this tutorial we learn how to install muscle package on Debian 12 using different package management tools: apt, apt-get and aptitude.
