IQ-TREE

IQ-TREE key features

IQ-TREE - Efficient Tree Reconstruction

A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time (Nguyen et al., 2015).

ModelFinder - Fast and Accurate Model Selection

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

UFBoot - Ultrafast Bootstrap Approximation

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

Big Data Analysis

Supporting huge datasets with thousands of sequences or millions of alignment sites via checkpointing, safe numerical and low memory mode. Multicore CPUs and parallel MPI system are utilized to speedup analysis.

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

W-IQ-TREE Web Service

User Support

The average response time is two working days.