How To Install spaced on Ubuntu 18.04
Introduction
In this tutorial we learn how to install spaced on Ubuntu 18.04.
What is spaced
spaced is:
Spaced (Words) is a new approach to alignment-free sequence comparison. While most alignment-free algorithms compare the word-composition of sequences, spaced uses a pattern of care and don’t care positions. The occurrence of a spaced word in a sequence is then defined by the characters at the match positions only, while the characters at the don’t care positions are ignored. Instead of comparing the frequencies of contiguous words in the input sequences, this new approach compares the frequencies of the spaced words according to the pre-defined pattern. An information-theoretic distance measure is then used to define pairwise distances on the set of input sequences based on their spaced-word frequencies. Systematic test runs on real and simulated sequence sets have shown that, for phylogeny reconstruction, this multiple-spaced-words approach is far superior to the classical alignment-free approach based on contiguous word frequencies.
There are three methods to install spaced on Ubuntu 18.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install spaced Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install spaced using apt-get by running the following command:
sudo apt-get -y install spaced
Install spaced Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install spaced using apt by running the following command:
sudo apt -y install spaced
Install spaced 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 spaced using aptitude by running the following command:
sudo aptitude -y install spaced
How To Uninstall spaced on Ubuntu 18.04
To uninstall only the spaced package we can use the following command:
sudo apt-get remove spaced
Uninstall spaced And Its Dependencies
To uninstall spaced and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove spaced
Remove spaced Configurations and Data
To remove spaced configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge spaced
Remove spaced configuration, data, and all of its dependencies
We can use the following command to remove spaced configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge spaced
References
Summary
In this tutorial we learn how to install spaced package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
