ModelGenerator: amino acid and nucleotide substitution model selection

ModelGenerator is a a free, easy-to-use model selection program, designed and written by Thomas Keane, that selects optimal amino acid and nucleotide substitution models from Fasta or Phylip alignments. ModelGenerator supports 56 nucleotide and 96 amino acid substitution models.

Modelgenerator uses the Akaike Information Criterion (AIC), the Bayesian Information Criterion (BIC) and hierarchical Likelihood-ratio tests (hLRTs) to select the best-fitting model of substitution.

ModelGenerator has been written using the Java programming language, and will easily run on any operating system supporting the Java VM.

ModelGenerator accepts both Fasta and Phylip format alignments. ModelGenerator uses the PAL library to perform its calculations

If you wish to receive the source code or have problems running ModelGenerator – email me:

Click on this link to download the file:


Startup command

java -jar modelgenerator.jar alignment_file num_gamma_categories
Modelgenerator is now part of the popular wEMBOSS package.

You should also check out our program for analysing site-to-site rate variation: TIGER

If you are interested in Phylogenetic Supertrees, then you might be interested in CLANN, which implements a variety of supertree methods.


Thomas M Keane, Christopher J Creevey , Melissa M Pentony, Thomas J Naughton and James O McInerney (2006) Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evolutionary Biology, 6:29


Some recent manuscripts that have cited ModelGenerator:

Declining transition/transversion ratios through time reveal limitations to the accuracy of nucleotide substitution models
S Duchne, SYW Ho, EC Holmes – BMC evolutionary biology, 2015

Mitochondrial genomes reveal the extinct Hippidion as an outgroup to all living equids
C Der Sarkissian, JT Vilstrup – Biology Letters, 2015

The performance of the date-randomisation test in phylogenetic analyses of time-structured virus data
S Duchne, D Duchne, EC Holmes, SYW Ho – Molecular biology and Evolution, 2015

ModelOMatic: fast and automated model selection between RY, nucleotide, amino acid, and codon substitution models
S Whelan, JE Allen, BP Blackburne – Systematic Biology, 2015

Empirical calibrated radiocarbon sampler: a tool for incorporating radiocarbon‐date and calibration error into Bayesian phylogenetic analyses of ancient DNA
M Molak, MA Suchard, SYW Ho – Molecular ecology, 2015

What behind these scales? Comments to “The complete mitochondrial genome of Temminck’s ground pangolin (Smutsia temminckii; Smuts, 1832) and phylogenetic …
P Gaubert, A Antunes – Gene, 2015

Independent origins of the feather lice (Insecta: Degeeriella) of raptors
TA Catanach, KP Johnson – Biological Journal of the Linnean society, 2015

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