How To Install maffilter on Ubuntu 22.04

In this tutorial we learn how to install maffilter on Ubuntu 22.04. maffilter is process genome alignment in the Multiple Alignment Format

Introduction

In this tutorial we learn how to install maffilter on Ubuntu 22.04.

What is maffilter

maffilter is:

MafFilter applies a series of “filters” to a MAF file, in order to clean it, extract data and computer statistics while keeping track of the associated meta-data such as genome coordinates and quality scores.

  • It can process the alignment to remove low-quality / ambiguous / masked regions.
  • It can export data into a single or multiple alignment file in format such as Fasta or Clustal.
  • It can read annotation data in GFF or GTF format, and extract the corresponding alignment.
  • It can perform sliding windows calculations.
  • It can reconstruct phylogeny/genealogy along the genome alignment.
  • It can compute population genetics statistics, such as site frequency spectrum, number of fixed/polymorphic sites, etc.

There are three methods to install maffilter 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 maffilter Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install maffilter using apt-get by running the following command:

sudo apt-get -y install maffilter

Install maffilter Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install maffilter using apt by running the following command:

sudo apt -y install maffilter

Install maffilter 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 maffilter using aptitude by running the following command:

sudo aptitude -y install maffilter

How To Uninstall maffilter on Ubuntu 22.04

To uninstall only the maffilter package we can use the following command:

sudo apt-get remove maffilter

Uninstall maffilter And Its Dependencies

To uninstall maffilter and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:

sudo apt-get -y autoremove maffilter

Remove maffilter Configurations and Data

To remove maffilter configuration and data from Ubuntu 22.04 we can use the following command:

sudo apt-get -y purge maffilter

Remove maffilter configuration, data, and all of its dependencies

We can use the following command to remove maffilter configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge maffilter

References

Summary

In this tutorial we learn how to install maffilter package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.