How To Install gapcleaner on Ubuntu 22.04

One-liner install command

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

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

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

What is gapcleaner and what are the ways to install it?

Before beginning this tutorial, you will need access to a server or computer running Ubuntu 22.04. This guide was written specifically with a server running Ubuntu 22.04 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 gapcleaner on Ubuntu 22.04. 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 gapcleaner 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 gapcleaner using apt by running the following command:

sudo apt -y install fsa

Install gapcleaner using apt

Because gapcleaner is available in Ubuntu 22.04’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 gapcleaner using apt by running the following command:

sudo apt -y install fsa

Install gapcleaner 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 22.04. Update apt database with aptitude using the following command.

sudo aptitude update

After updating aptitude database, You can install gapcleaner by running the following command:

sudo aptitude -y install fsa

How to upgrade (update) a single package gapcleaner 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 gapcleaner, e.g. single package, you should use the following format with the apt-get command/apt command:

sudo apt-get --only-upgrade install fsa

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 fsa

How To Uninstall gapcleaner from Ubuntu 22.04

To uninstall only the gapcleaner package you can execute the following command:

sudo apt-get remove fsa

Uninstall gapcleaner and all its dependencies

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

sudo apt-get -y autoremove fsa

Remove gapcleaner with all configurations and data

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

sudo apt-get -y purge fsa

Remove gapcleaner completely (configurations, data and all of its dependencies)

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

sudo apt-get -y autoremove --purge fsa

Extra info and code examples

FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences. Much as distance-based phylogenetic reconstruction methods like Neighbor-Joining build a phylogeny using only pairwise divergence estimates, FSA builds a multiple alignment using only pairwise estimations of homology. This is made possible by the sequence annealing technique for constructing a multiple alignment from pairwise comparisons, developed by Ariel Schwartz. FSA brings the high accuracies previously available only for small-scale analyses of proteins or RNAs to large-scale problems such as aligning thousands of sequences or megabase-long sequences. FSA introduces several novel methods for constructing better alignments: * FSA uses machine-learning techniques to estimate gap and substitution parameters on the fly for each set of input sequences. This "query-specific learning" alignment method makes FSA very robust: it can produce superior alignments of sets of homologous sequences which are subject to very different evolutionary constraints. * FSA is capable of aligning hundreds or even thousands of sequences using a randomized inference algorithm to reduce the computational cost of multiple alignment. This randomized inference can be over ten times faster than a direct approach with little loss of accuracy. * FSA can quickly align very long sequences using the "anchor annealing" technique for resolving anchors and projecting them with transitive anchoring. It then stitches together the alignment between the anchors using the methods described above. * The included GUI, MAD (Multiple Alignment Display), can display the intermediate alignments produced by FSA, where each character is colored according to the probability that it is correctly aligned

Conclusion

You now have a full guide on how to install gapcleaner using apt, apt-get and aptitude tools. Also, we showed how to update as a single package and different ways to uninstall the gapcleaner from Ubuntu 22.04.

See also: