How To Install fsa on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 585 words
Introduction
In this tutorial we learn how to install fsa on Ubuntu.
What is fsa
fsa is:
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
There are three methods to install fsa on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install fsa Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install fsa using apt-get by running the following command:
sudo apt-get -y install fsa
Install fsa Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install fsa using apt by running the following command:
sudo apt -y install fsa
Install fsa 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 fsa using aptitude by running the following command:
sudo aptitude -y install fsa
How To Uninstall fsa on Ubuntu
To uninstall only the fsa package we can use the following command:
sudo apt-get remove fsa
Uninstall fsa And Its Dependencies
To uninstall fsa and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove fsa
Remove fsa Configurations and Data
To remove fsa configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge fsa
Remove fsa configuration, data, and all of its dependencies
We can use the following command to remove fsa configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge fsa
Dependencies
fsa have the following dependencies:
References
Summary
In this tutorial we learn how to install fsa package on Ubuntu using different package management tools: apt, apt-get and aptitude.