How To Install quicktree on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
2 minutes • 422 words
Introduction
In this tutorial we learn how to install quicktree on Ubuntu.
What is quicktree
quicktree is:
QuickTree is an efficient implementation of the Neighbor-Joining algorithm (PMID: 3447015), capable of reconstructing phylogenies from huge alignments in time less than the age of the universe.
QuickTree accepts both distance matrix and multiple-sequence-aligment inputs. The former should be in PHYLIP format. The latter should be in Stockholm format, which is the native alignment format for the Pfam database. Alignments in various formats can be converted to Stockholm format with the sreformat program, which is part of the HMMer package (hmmer.org).
The tress are written to stdout, in the Newick/New-Hampshire format use by PHYLIP and many other programs
There are three methods to install quicktree 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 quicktree Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install quicktree using apt-get by running the following command:
sudo apt-get -y install quicktree
Install quicktree Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install quicktree using apt by running the following command:
sudo apt -y install quicktree
Install quicktree 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 quicktree using aptitude by running the following command:
sudo aptitude -y install quicktree
How To Uninstall quicktree on Ubuntu
To uninstall only the quicktree package we can use the following command:
sudo apt-get remove quicktree
Uninstall quicktree And Its Dependencies
To uninstall quicktree and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove quicktree
Remove quicktree Configurations and Data
To remove quicktree configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge quicktree
Remove quicktree configuration, data, and all of its dependencies
We can use the following command to remove quicktree configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge quicktree
Dependencies
quicktree have the following dependencies:
References
Summary
In this tutorial we learn how to install quicktree package on Ubuntu using different package management tools: apt, apt-get and aptitude.