How To Install iqtree on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 459 words
Introduction
In this tutorial we learn how to install iqtree on Ubuntu.
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 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 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 Ubuntu. 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 Ubuntu
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 Ubuntu, we can use the command below:
sudo apt-get -y autoremove iqtree
Remove iqtree Configurations and Data
To remove iqtree configuration and data from Ubuntu 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 Ubuntu using different package management tools: apt, apt-get and aptitude.