Gene

Tree (set theory)

Machine learning

Mathematical analysis

Artificial intelligence

Phylogenetic tree

Programming language

Phylogenetic network

Inference

Software

Mathematics

Computer science

Tree rearrangement

Genetics

Computational biology

Evolutionary biology

Biology

Molecular Biology and Evolution

IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era