How To Install python3-edlib on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 475 words
Introduction
In this tutorial we learn how to install python3-edlib on Ubuntu.
What is python3-edlib
python3-edlib is:
A lightweight and super fast C/C++ library for sequence alignment using edit distance.
Calculating edit distance of two strings is as simple as:
edlibAlign(“hello”, 5, “world!”, 6, edlibDefaultAlignConfig()).editDistance; Features
- Calculates edit distance (Levehnstein distance).
- It can find optimal alignment path (instructions how to transform first sequence into the second sequence).
- It can find just the start and/or end locations of alignment path - can be useful when speed is more important than having exact alignment path.
- Supports multiple alignment methods: global(NW), prefix(SHW) and infix(HW), each of them useful for different scenarios.
- You can extend character equality definition, enabling you to e.g. have wildcard characters, to have case insensitive alignment or to work with degenerate nucleotides.
- It can easily handle small or very large sequences, even when finding alignment path, while consuming very little memory.
- Super fast thanks to Myers’s bit-vector algorithm.
This package contains the Python3 module.
There are three methods to install python3-edlib 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 python3-edlib Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install python3-edlib using apt-get by running the following command:
sudo apt-get -y install python3-edlib
Install python3-edlib Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install python3-edlib using apt by running the following command:
sudo apt -y install python3-edlib
Install python3-edlib 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 python3-edlib using aptitude by running the following command:
sudo aptitude -y install python3-edlib
How To Uninstall python3-edlib on Ubuntu
To uninstall only the python3-edlib package we can use the following command:
sudo apt-get remove python3-edlib
Uninstall python3-edlib And Its Dependencies
To uninstall python3-edlib and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove python3-edlib
Remove python3-edlib Configurations and Data
To remove python3-edlib configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge python3-edlib
Remove python3-edlib configuration, data, and all of its dependencies
We can use the following command to remove python3-edlib configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge python3-edlib
Dependencies
python3-edlib have the following dependencies:
References
Summary
In this tutorial we learn how to install python3-edlib package on Ubuntu using different package management tools: apt, apt-get and aptitude.