Using IQ-Tree

Introduction

IQ-TREE is relatively recent (2014) open-source software package for phylogenetic inference using the maximum likelihood (ML) criterion. It has a very good performance when compared with other popular ML phylogenetics software such as RAxML and PhyML, and it has been playing a vital role as an integral component for many platforms such as Nextstrain (Minh et al. 2020). According to this latter publication:

The high performance of IQ-TREE results from the efficient integration of novel phylogenetic methods that improve the three key steps in phylogenetic analysis: fast model selection via ModelFinder, an effective tree search algorithm, and a novel ultrafast bootstrap approximation.

IQ-Tree is also good for phylogenomics analyzes, since it t also finds the best-fit partitioning scheme for your dataset, allowing complex models for mixed data types, mixed rate heterogeneity types, linked or unlinked branch lengths. In addition, its fast Maximum Likelihood and bootstraps implementations make this application a must have in phylogenetics hypothesis testing.

The Tutorial

The IQ-Tree site has a very good beginner tutorial, which we are going to use on this course. The tutorial can accessed by the following link:

http://www.iqtree.org/workshop/sydney2022

We can also use the Web Server tutorial described by the following link:

http://www.iqtree.org/doc/Web-Server-Tutorial

Documentation

IQ-Tree has a very thoroughly manual, which describes how to perform since simple tasks, like changing sequence formats, to apply complex models to phylogenomics datasets. Please find bellow the direct link for the IQ-Tree manual:

-http://www.iqtree.org/doc/iqtree-doc.pdf

IQ-TREE has an extensive documentation with several tutorials and manual (copied from IQ-Tree website):