How To Install repeat-match on Kali Linux

One-liner install command

For those in a hurry, here's a one-line installation command:

sudo apt-get update && sudo apt -y install mummer

But if you are interested in the detailed steps with descriptions, the following information is for you.

What is repeat-match and what are the ways to install it?

Before beginning this tutorial, you will need access to a server or computer running Kali Linux. This guide was written specifically with a server running Kali Linux in mind, although it should also work on older, supported versions of the operating system.

Also, make sure you are running a regular, non-root user with sudo privileges configured on your server. When you have an account available, log in as your non-root user to begin.

There are several ways to install repeat-match on Kali Linux. You can use (links are clickable):

In the following sections, we will describe each method in detail. You can choose one of them or refer to the recommended one.

Install repeat-match using apt-get

First, update apt database with apt-get using the following command.

sudo apt-get update

After updating apt-get database, You can install repeat-match using apt by running the following command:

sudo apt -y install mummer

Install repeat-match using apt

Because repeat-match is available in Kali Linux’s default repositories, it is possible to install it from these repositories using the apt packaging system.

To begin, update apt database with apt using the following command.

sudo apt update

After updating apt database, You can install repeat-match using apt by running the following command:

sudo apt -y install mummer

Install repeat-match 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 Kali Linux. Update apt database with aptitude using the following command.

sudo aptitude update

After updating aptitude database, You can install repeat-match by running the following command:

sudo aptitude -y install mummer

How to upgrade (update) a single package repeat-match using apt-get?

First, you will need to update packages index. Run update command as usual:

sudo apt-get update

Next, to upgrade only the repeat-match, e.g. single package, you should use the following format with the apt-get command/apt command:

sudo apt-get --only-upgrade install mummer

Note that this command will not install any new packages! If you wish to install the package if it doesn't exist you may leave out --only-upgrade part.

sudo apt-get install mummer

How To Uninstall repeat-match from Kali Linux

To uninstall only the repeat-match package you can execute the following command:

sudo apt-get remove mummer

Uninstall repeat-match and all its dependencies

To uninstall repeat-match and its dependencies that are no longer needed by Kali Linux, you can use the command below:

sudo apt-get -y autoremove mummer

Remove repeat-match with all configurations and data

To remove repeat-match configuration and data from your system you can run the following purge command:

sudo apt-get -y purge mummer

Remove repeat-match completely (configurations, data and all of its dependencies)

And lastly, you can run the next command to remove absolutely everything related to repeat-match package, e.g.: configurations, data and all of its dependencies. Just use this command:

sudo apt-get -y autoremove --purge mummer

Extra info and code examples

MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it handles the 100s or 1000s of contigs from a shotgun sequencing project with ease, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences.

Conclusion

You now have a full guide on how to install repeat-match using apt, apt-get and aptitude tools. Also, we showed how to update as a single package and different ways to uninstall the repeat-match from Kali Linux.

See also: