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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 (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 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).
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.
All common substitution models for DNA, protein, codon, binary and morphological data with rate heterogeneity among sites.
Phylogenomic partition models allowing for mixed data types, mixed rate heterogeneity types, linked or unlinked branch lengths.
Mixture models such as empirical protein mixture models and customizable mixture models.
The average response time is two working days.
The stable IQ-TREE version 1.6.12 (August 15, 2019)
COVID-19 release 2.2.0 (March 25, 2022)