How To Install fasttree on Debian 11
Introduction
In this tutorial we learn how to install fasttree on Debian 11.
What is fasttree
fasttree is:
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. It handles alignments with up to a million of sequences in a reasonable amount of time and memory. For large alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or RAxML 7.
FastTree is more accurate than PhyML 3 with default settings, and much more accurate than the distance-matrix methods that are traditionally used for large alignments. FastTree uses the Jukes-Cantor or generalized time-reversible (GTR) models of nucleotide evolution and the JTT (Jones-Taylor-Thornton 1992) model of amino acid evolution. To account for the varying rates of evolution across sites, FastTree uses a single rate for each site (the “CAT” approximation). To quickly estimate the reliability of each split in the tree, FastTree computes local support values with the Shimodaira-Hasegawa test (these are the same as PhyML 3’s “SH-like local supports”).
This package contains a single threaded version (fasttree) and a parallel version which uses OpenMP (fasttreMP).
There are three methods to install fasttree on Debian 11. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install fasttree Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install fasttree using apt-get by running the following command:
sudo apt-get -y install fasttree
Install fasttree Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install fasttree using apt by running the following command:
sudo apt -y install fasttree
Install fasttree 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 Debian. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install fasttree using aptitude by running the following command:
sudo aptitude -y install fasttree
How To Uninstall fasttree on Debian 11
To uninstall only the fasttree package we can use the following command:
sudo apt-get remove fasttree
Uninstall fasttree And Its Dependencies
To uninstall fasttree and its dependencies that are no longer needed by Debian 11, we can use the command below:
sudo apt-get -y autoremove fasttree
Remove fasttree Configurations and Data
To remove fasttree configuration and data from Debian 11 we can use the following command:
sudo apt-get -y purge fasttree
Remove fasttree configuration, data, and all of its dependencies
We can use the following command to remove fasttree configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge fasttree
Dependencies
fasttree have the following dependencies:
References
Summary
In this tutorial we learn how to install fasttree package on Debian 11 using different package management tools: apt, apt-get and aptitude.
