How To Install fasttree on Kali Linux

In this tutorial we learn how to install fasttree on Kali Linux. fasttree is phylogenetic trees from alignments of nucleotide or protein sequences

Introduction

In this tutorial we learn how to install fasttree on Kali Linux.

What is fasttree

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 ways to install fasttree on Kali Linux . 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 Kali Linux. 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 Kali Linux

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 Kali Linux, we can use the command below:

sudo apt-get -y autoremove fasttree

Remove fasttree Configurations and Data

To remove fasttree configuration and data from Kali Linux 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

References

Summary

In this tutorial we learn how to install fasttree using different package management tools like apt, apt-get and aptitude.