How To Install iqtree on Debian 12

Learn how to install iqtree on Debian 12 with this tutorial. iqtree is efficient phylogenetic software by maximum likelihood

Introduction

In this tutorial we learn how to install iqtree on Debian 12.

What is iqtree

iqtree is:

IQ-TREE is a very efficient maximum likelihood phylogenetic software with following key features among others:

  • A novel fast and effective stochastic algorithm to estimate maximum likelihood trees. IQ-TREE outperforms both RAxML and PhyML in terms of likelihood while requiring similar amount of computing time (see Nguyen et al., 2015)
  • An ultrafast bootstrap approximation to assess branch supports (see Minh et al., 2013).
  • A wide range of substitution models for binary, DNA, protein, codon, and morphological alignments.
  • Ultrafast model selection for all data types, 10 to 100 times faster than jModelTest and ProtTest.
  • Finding best partition scheme like PartitionFinder.
  • Partitioned models with mixed data types for phylogenomic (multi- gene) alignments, allowing for separate, proportional, or joint branch lengths among genes.
  • Supporting the phylogenetic likelihod library (PLL) (see Flouri et al., 2014)

There are three methods to install iqtree on Debian 12. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install iqtree Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install iqtree using apt-get by running the following command:

sudo apt-get -y install iqtree

Install iqtree Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install iqtree using apt by running the following command:

sudo apt -y install iqtree

Install iqtree 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 iqtree using aptitude by running the following command:

sudo aptitude -y install iqtree

How To Uninstall iqtree on Debian 12

To uninstall only the iqtree package we can use the following command:

sudo apt-get remove iqtree

Uninstall iqtree And Its Dependencies

To uninstall iqtree and its dependencies that are no longer needed by Debian 12, we can use the command below:

sudo apt-get -y autoremove iqtree

Remove iqtree Configurations and Data

To remove iqtree configuration and data from Debian 12 we can use the following command:

sudo apt-get -y purge iqtree

Remove iqtree configuration, data, and all of its dependencies

We can use the following command to remove iqtree configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge iqtree

Dependencies

iqtree have the following dependencies:

References

Summary

In this tutorial we learn how to install iqtree package on Debian 12 using different package management tools: apt, apt-get and aptitude.