ModelFinder

ModelFinder is a model selection tool used in phylogenetic analysis to identify the best-fitting model of sequence evolution for a given alignment. It is integrated into the IQ-TREE software package and is widely used in molecular systematics and phylogenomics to inform downstream tree inference.

The tool evaluates a large set of substitution models for both nucleotide and amino acid data, including common nucleotide models such as JC, HKY, and GTR, and several amino acid models such as JTT, WAG, and LG. It can account for rate variation across sites by incorporating gamma-distributed rates and/or a proportion of invariable sites, and it can utilize empirical base or amino acid frequencies. For larger analyses, it can be used in conjunction with partitioning schemes. ModelFinder compares models using information criteria such as AIC, AICc, and BIC to rank models and select the best-fitting one.

The output includes the best model and its estimated parameters, which can be used directly in IQ-TREE to perform maximum-likelihood tree inference with the chosen model. The tool is designed to be fast and scalable, enabling model selection for large alignments and datasets.

ModelFinder’s role is to improve phylogenetic inference by providing objective, automated model choice, reducing user bias and manual trial-and-error. It is widely cited in phylogenetic studies and commonly used in pipeline analyses; however, model choice may be influenced by data size, composition, and alignment quality and may not guarantee improved results in all cases.