IQ-TREE

IQ-TREE feature highlights

IQ-TREE - Efficient Tree Reconstruction

A fast search algorithm (Nguyen et al., 2015) to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML.

ModelFinder - Fast and Accurate Model Selection

ModelFinder (Kalyaanamoorthy et al., 2017) is 10 to 100 times faster than jModelTest and ProtTest. It also finds best-fit partitioning scheme like PartitionFinder.

UFBoot - Ultrafast Bootstrap Approximation

UFBoot (Minh et al., 2013) provides approximately unbiased branch support values and runs 100X faster than nonparametric bootstrap and 10 to 40 times faster than RAxML rapid bootstrap.

AliSim - Alignment Simulator New!

AliSim (Ly-Trong et al., 2023) allows to quickly simulate multiple sequence alignments under more realistic models than Seq-Gen and INDELible.

IQ-TREE supports a wide range of evolutionary models

Common Models

All common substitution models for DNA, protein, codon, binary and morphological data with rate heterogeneity among sites.

Partition Models

Phylogenomic partition models allowing for mixed data types, mixed rate heterogeneity types, linked or unlinked branch lengths.

Mixture Models

Mixture models such as empirical protein mixture models and customizable mixture models.

IQ-TREE is user-friendly and well-documented

Online Web Service

User Support