ModelGenerator: amino acid and nucleotide substitution model selection in phylogenetics.
ModelGenerator is a free easy-to-use software program for carrying out model selection in phylogenetics, designed and written by Thomas Keane.
ModelGenerator is a model selection program 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: drtkeane_at_gmail.com
Click on this link to download the file:
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:
The evolution of mitochondrial genomes in subterranean caviomorph rodents: Adaptation against a background of purifying selection Author(s): Tomasco Ivanna H.; Lessa Enrique P. MOLECULAR PHYLOGENETICS AND EVOLUTION Volume: 61 Issue: 1 Pages: 64-70 DOI: 10.1016/j.ympev.2011.06.014 Published: OCT 2011
Domain Loss Facilitates Accelerated Evolution and Neofunctionalization of Duplicate Snake Venom Metalloproteinase Toxin Genes Author(s): Casewell Nicholas R.; Wagstaff Simon C.; Harrison Robert A.; et al. MOLECULAR BIOLOGY AND EVOLUTION Volume: 28 Issue: 9 Pages: 2637-2649 DOI: 10.1093/molbev/msr091 Published: SEP 2011
Signatures of selection and sex-specific expression variation of a novel duplicate during the evolution of the Drosophila desaturase gene family Author(s): Keays Maria C.; Barker Daniel; Wicker-Thomas Claude; et al. MOLECULAR ECOLOGY Volume: 20 Issue: 17 Pages: 3617-3630 DOI: 10.1111/j.1365-294X.2011.05208.x Published: SEP 2011
Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional and separate models for combined molecular phylogenetic analyses of multilocus sequence data Author(s): Tanabe Akifumi S. MOLECULAR ECOLOGY RESOURCES Volume: 11 Issue: 5 Pages: 914-921 DOI: 10.1111/j.1755-0998.2011.03021.x Published: SEP 2011
Geographical and seasonal evidence of cryptic diversity in the Baetis rhodani complex (Ephemeroptera, Baetidae) revealed by means of DNA taxonomy Author(s): Lucentini Livia; Rebora Manuela; Puletti Maria Elena; et al. HYDROBIOLOGIA Volume: 673 Issue: 1 Pages: 215-228 DOI: 10.1007/s10750-011-0778-1 Published: SEP 2011
Cardicola opisthorchis n. sp. (Trematoda: Aporocotylidae) from the Pacific bluefin tuna, Thunnus orientalis (Temminck & Schlegel, 1844), cultured in Japan Author(s): Ogawa K.; Ishimaru K.; Shirakashi S.; et al. PARASITOLOGY INTERNATIONAL Volume: 60 Issue: 3 Pages: 307-312 DOI: 10.1016/j.parint.2011.05.002 Published: SEP 2011
Freshwater sponge silicateins: Comparison of gene sequences and exon-intron structure Author(s): Kalyuzhnaya O. V.; Krasko A. G.; Grebenyuk V. A.; et al. MOLECULAR BIOLOGY Volume: 45 Issue: 4 Pages: 567-575 DOI: 10.1134/S002689331103006X Published: AUG 2011
Complicated evolution of the caprellid (Crustacea: Malacostraca: Peracarida: Amphipoda) body plan, reacquisition or multiple losses of the thoracic limbs and pleons Author(s): Ito Atsushi; Aoki Masakazu N.; Yahata Kensuke; et al.Source: DEVELOPMENT GENES AND EVOLUTION Volume: 221 Issue: 3 Pages: 133-140 DOI: 10.1007/s00427-011-0365-5 Published: AUG 2011
Analysis of global and local population stratification of finless porpoises Neophocaena phocaenoides in Chinese waters Author(s): Li Xiang; Liu Yingying; Tzika Athanasia C.; et al.Source: MARINE BIOLOGY Volume: 158 Issue: 8 Pages: 1791-1804 DOI: 10.1007/s00227-011-1692-9 Published: AUG 2011