iqtree

IQ-TREE infers phylogenetic trees using maximum likelihood methods for large-scale phylogenomic datasets.

Key Features:

• Stochastic search algorithm: Employs a combination of hill-climbing approaches and stochastic perturbation methods to explore phylogenetic tree space efficiently.
• Performance efficiency: Achieves higher likelihoods than RAxML and PhyML in 62.2%–87.1% of studied alignments under equivalent CPU time allowances.
• Adaptive stopping rule: Implements an adaptive stopping criterion that yields higher likelihoods in 73.3%–97.1% of cases using IQ-TREE's rule, while RAxML and PhyML can be faster for certain datasets (RAxML faster in 75.7% of DNA alignments and 47.1% of protein alignments; PhyML faster in 100% of protein alignments).

Scientific Applications:

• Large-scale phylogenomic inference: Performs rapid and accurate maximum-likelihood tree estimation for both DNA and protein alignments.
• Evolutionary biology, molecular genetics, and comparative genomics: Supports inference of evolutionary relationships across genes, species, and genomes for comparative and evolutionary analyses.

Methodology:

Performs maximum-likelihood phylogenetic inference using hill-climbing optimization combined with stochastic perturbations and an adaptive stopping rule.