TNT, a free program for phylogenetic analysis
Open accessAbstract
The main features of the phylogeny program TNT are discussed. Windows versions have a menu interface, while Macintosh and Linux versions are command‐driven. The program can analyze data sets with discrete (additive, non‐additive, step‐matrix) as well as continuous characters (evaluated with Farris optimization). Effective analysis of large data sets can be carried out in reasonable times, and a number of methods to help identifying wildcard taxa in the case of ambiguous data sets are implemented. A variety of methods for diagnosing trees and exploring character evolution is available in TNT, and publication‐quality tree‐diagrams can be saved as metafiles. Through the use of a number of native commands and a simple but powerful scripting language, TNT allows the user an enormous flexibility in phylogenetic analyses or simulations. © The Willi Hennig Society 2008.
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Cites
Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology
Fitch, W. M. (1971) · Systematic Biology · doi:10.1093/sysbio/20.4.406 · Cited by 7,690 · see citing works
Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology
Fitch, W. M. (1971) · Systematic Zoology · doi:10.2307/2412116 · Cited by 5,661 · see citing works
TESTING SIGNIFICANCE OF INCONGRUENCE
Farris, J. S., Källersjö, M., Kluge, A. G., & Bult, C. J. (1994) · Cladistics · doi:10.1111/j.1096-0031.1994.tb00181.x · Cited by 3,875 · see citing works
Self-citationComparison of phylogenetic trees
Robinson, D. F., & Foulds, L. R. (1981) · Mathematical Biosciences · doi:10.1016/0025-5564(81)90043-2 · Cited by 2,990 · see citing works
The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis
Nixon, K. C. (1999) · Cladistics · doi:10.1111/j.1096-0031.1999.tb00277.x · Cited by 1,748 · see citing works
Self-citationTHE RETENTION INDEX AND THE RESCALED CONSISTENCY INDEX
Farris, J. S. (1989) · Cladistics · doi:10.1111/j.1096-0031.1989.tb00573.x · Cited by 1,645 · see citing works
Self-citationPARSIMONY JACKKNIFING OUTPERFORMS NEIGHBOR‐JOINING
Farris, J. S., Albert, V. A., Källersjö, M., Lipscomb, D., & Kluge, A. G. (1996) · Cladistics · doi:10.1111/j.1096-0031.1996.tb00196.x · Cited by 1,512 · see citing works
Self-citationEstimating character weights during tree search
Goloboff, P. A. (1993) · Cladistics · doi:10.1111/j.1096-0031.1993.tb00209.x · Cited by 1,296 · see citing works
Self-citationA Successive Approximations Approach to Character Weighting
Farris, J. S. (1969) · Systematic Zoology · doi:10.2307/2412182 · Cited by 1,286 · see citing works
Self-citationMethods for Computing Wagner Trees
Farris, J. S. (1970) · Systematic Biology · doi:10.1093/sysbio/19.1.83 · Cited by 1,243 · see citing works
Self-citationAnalyzing large data sets in reasonable times: solutions for composite optima
Goloboff, P. A. (1999) · Cladistics · doi:10.1111/j.1096-0031.1999.tb00278.x · Cited by 1,039 · see citing works
Self-citationMethods for Computing Wagner Trees
Farris, J. S. (1970) · Systematic Zoology · doi:10.2307/2412028 · Cited by 937 · see citing works
Self-citationImprovements to resampling measures of group support
Goloboff, P. A., Farris, J. S., Källersjö, M., Oxelman, B., Ramıacute;rez, M. J., & Szumik, C. A. (2003) · Cladistics · doi:10.1111/j.1096-0031.2003.tb00376.x · Cited by 851 · see citing works
Self-citationT.N.T.: Tree Analysis Using New Technology
Goloboff, P. A., Farris, J., & Nixon, K. C. (2003) · Cited by 771 · see citing works
Self-citationContinuous characters analyzed as such
Goloboff, P. A., Mattoni, C. I., & Quinteros, A. S. (2006) · Cladistics · doi:10.1111/j.1096-0031.2006.00122.x · Cited by 421 · see citing works
Self-citationParsimony, Phylogeny, and Genomics
Albert, V. A. (2006) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199297306.001.0001 · Cited by 357 · see citing works
TNT: Tree Analysis Using New Technology
Giribet, G. (2005) · Systematic Biology · doi:10.1080/10635150590905830 · Cited by 346 · see citing works
Methods for quick consensus estimation
Goloboff, P. (2001) · Cladistics · doi:10.1006/clad.2000.0156 · Cited by 274 · see citing works
Self-citationLocating the vertices of a steiner tree in an arbitrary metric space
Sankoff, D., & Rousseau, P. (1975) · Mathematical Programming · doi:10.1007/bf01681346 · Cited by 264 · see citing works
Methods for Quick Consensus Estimation
Goloboff, P. A., & Farris, J. S. (2001) · Cladistics · doi:10.1111/j.1096-0031.2001.tb00102.x · Cited by 255 · see citing works
Self-citationPROBLEMS WITH ZERO‐LENGTH BRANCHES
Coddington, J. A., & Scharff, N. (1994) · Cladistics · doi:10.1111/j.1096-0031.1994.tb00187.x · Cited by 241 · see citing works
Phylogenetic Supermatrix Analysis of GenBank Sequences from 2228 Papilionoid Legumes
McMahon, M. M., & Sanderson, M. J. (2006) · Systematic Biology · doi:10.1080/10635150600999150 · Cited by 177 · see citing works
On Comparing the Shapes of Taxonomic Trees
Farris, J. S. (1973) · Systematic Zoology · doi:10.2307/2412378 · Cited by 128 · see citing works
Self-citationGoloboff, P. A. (1997) · Cladistics · doi:10.1111/j.1096-0031.1997.tb00317.x · Cited by 107 · see citing works
Self-citationCalculating SPR distances between trees
Goloboff, P. A. (2007) · Cladistics · doi:10.1111/j.1096-0031.2007.00189.x · Cited by 99 · see citing works
Self-citation[38] Phylogeny determination using dynamically weighted parsimony method
Williams, P. L., & Fitch, W. M. (1990) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/0076-6879(90)83040-g · Cited by 91 · see citing works
METHODS FOR FASTER PARSIMONY ANALYSIS
Goloboff, P. A. (1996) · Cladistics · doi:10.1006/clad.1996.0015 · Cited by 83 · see citing works
Self-citationMETHODS FOR FASTER PARSIMONY ANALYSIS
Goloboff, P. A. (1996) · Cladistics · doi:10.1111/j.1096-0031.1996.tb00009.x · Cited by 83 · see citing works
Self-citationGoloboff, P. A., & Pol, D. (2002) · Cladistics · doi:10.1016/s0748-3007(02)00117-2 · Cited by 66 · see citing works
Self-citationGoloboff, P. A., & Pol, D. (2002) · Cladistics · doi:10.1111/j.1096-0031.2002.tb00289.x · Cited by 58 · see citing works
Self-citationThe limits of conventional cladistic analysis
Davis, J. I., Nixon, K. C., & Little, D. P. (2006) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199297306.003.0007 · Cited by 23 · see citing works
Self-citationMeier, R., & Ali, F. (2005) · Systematic Entomology · doi:10.1111/j.1365-3113.2005.00297.x · Cited by 22 · see citing works
Parsimony overcomes statistical inconsistency with the addition of more data from the same gene
Pickett, K. M., Tolman, G. L., Wheeler, W. C., & Wenzel, J. W. (2005) · Cladistics · doi:10.1111/j.1096-0031.2005.00076.x · Cited by 22 · see citing works
On Divide-and-Conquer Strategies for Parsimony Analysis of Large Data Sets: Rec-I-DCM3 versus TNT
Goloboff, P. A., & Pol, D. (2007) · Systematic Biology · doi:10.1080/10635150701431905 · Cited by 20 · see citing works
Self-citationFarris, J. S. (2001) · Cladistics · doi:10.1111/j.1096-0031.2001.tb00133.x · Cited by 13 · see citing works
Self-citation
Flagged first, then by citations
Research works printed but not linked: 1
- Hovenkamp, P., 2004. Review of TNT-Tree analysis using New Technology, ver. 1.0. Cladistics 20, 378-383.
Cited by
Sorted by citations
Whole-genome analyses resolve early branches in the tree of life of modern birds
Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., Ho, S. Y. W., Faircloth, B. C., Nabholz, B., Howard, J. T., et al. (2014) · Science · doi:10.1126/science.1253451 · Cited by 1,901 · see citing works
Phylotranscriptomic analysis of the origin and early diversification of land plants
Wickett, N. J., Mirarab, S., Nguyen, N., Warnow, T., Carpenter, E., Matasci, N., Ayyampalayam, S., Barker, M. S., Burleigh, J. G., Gitzendanner, M. A., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1323926111 · Cited by 1,252 · see citing works
A Review of Dromaeosaurid Systematics and Paravian Phylogeny
Turner, A. H., Makovicky, P. J., & Norell, M. A. (2012) · Bulletin of the American Museum of Natural History · doi:10.1206/748.1 · Cited by 350 · see citing works
Brusatte, S. L., Lloyd, G. T., Wang, S. C., & Norell, M. A. (2014) · Current Biology · doi:10.1016/j.cub.2014.08.034 · Cited by 313 · see citing works
An Archaeopteryx-like theropod from China and the origin of Avialae
Xu, X., You, H., Du, K., & Han, F. (2011) · Nature · doi:10.1038/nature10288 · Cited by 314 · see citing works
Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life
Arcila, D., Ortí, G., Vari, R., Armbruster, J. W., Stiassny, M. L. J., Ko, K. D., Sabaj, M. H., Lundberg, J., Revell, L. J., & Betancur-R., R. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-016-0020 · Cited by 243 · see citing works
Goloboff, P. A. (2014) · Cladistics · doi:10.1111/cla.12047 · Cited by 248 · see citing works
Self-citationComplete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear
Lindqvist, C., Schuster, S. C., Sun, Y., Talbot, S. L., Qi, J., Ratan, A., Tomsho, L. P., Kasson, L., Zeyl, E., Aars, J., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0914266107 · Cited by 193 · see citing works
Synchrotron scanning reveals amphibious ecomorphology in a new clade of bird-like dinosaurs
Cau, A., Beyrand, V., Voeten, D. F. A. E., Fernandez, V., Tafforeau, P., Stein, K., Barsbold, R., Tsogtbaatar, K., Currie, P. J., & Godefroit, P. (2017) · Nature · doi:10.1038/nature24679 · Cited by 173 · see citing works
Dating tips for divergence time estimation
O’Reilly, J. E., dos Reis, M., & Donoghue, P. C. J. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.08.001 · Cited by 159 · see citing works
Pre‐modern Birds: Avian Divergences in the Mesozoic
O'Connor, J., Chiappe, L. M., & Bell, A. (2011) · Living Dinosaurs · doi:10.1002/9781119990475.ch3 · Cited by 163 · see citing works
Terraces in phylogenetic tree space
Sanderson, M. J., McMahon, M. M., & Steel, M. (2011) · Science · doi:10.1126/science.1206357 · Cited by 144 · see citing works
Potential for Powered Flight Neared by Most Close Avialan Relatives, but Few Crossed Its Thresholds
Pei, R., Pittman, M., Goloboff, P. A., Dececchi, T. A., Habib, M. B., Kaye, T. G., Larsson, H. C. E., Norell, M. A., Brusatte, S. L., & Xu, X. (2020) · Current Biology · doi:10.1016/j.cub.2020.06.105 · Cited by 137 · see citing works
Self-citationReduced plumage and flight ability of a new Jurassic paravian theropod from China
Godefroit, P., Demuynck, H., Dyke, G., Hu, D., Escuillié, F., & Claeys, P. (2013) · Nature Communications · doi:10.1038/ncomms2389 · Cited by 124 · see citing works
Gao, C., Morschhauser, E. M., Varricchio, D. J., Liu, J., & Zhao, B. (2012) · PLoS ONE · doi:10.1371/journal.pone.0045203 · Cited by 96 · see citing works
Zhao, Y., Vinther, J., Parry, L. A., Wei, F., Green, E., Pisani, D., Hou, X., Edgecombe, G. D., & Cong, P. (2019) · Current Biology · doi:10.1016/j.cub.2019.02.036 · Cited by 89 · see citing works
Mosaic evolution in an asymmetrically feathered troodontid dinosaur with transitional features
Xu, X., Currie, P., Pittman, M., Xing, L., Meng, Q., Lü, J., Hu, D., & Yu, C. (2017) · Nature Communications · doi:10.1038/ncomms14972 · Cited by 86 · see citing works
Fuxianhuiid ventral nerve cord and early nervous system evolution in Panarthropoda
Yang, J., Ortega-Hernández, J., Butterfield, N. J., Liu, Y., Boyan, G. S., Hou, J.-B., Lan, T., & Zhang, X.-G. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1522434113 · Cited by 87 · see citing works
Lü, J., & Brusatte, S. L. (2015) · Scientific Reports · doi:10.1038/srep11775 · Cited by 74 · see citing works
Goloboff, P. A., & Szumik, C. A. (2015) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2015.04.003 · Cited by 73 · see citing works
Self-citationA new Jurassic theropod from China documents a transitional step in the macrostructure of feathers
Lefèvre, U., Cau, A., Cincotta, A., Hu, D., Chinsamy, A., Escuillié, F., & Godefroit, P. (2017) · The Science of Nature · doi:10.1007/s00114-017-1496-y · Cited by 62 · see citing works
Re-evaluation of the Haarlem Archaeopteryx and the radiation of maniraptoran theropod dinosaurs
Foth, C., & Rauhut, O. W. M. (2017) · BMC Evolutionary Biology · doi:10.1186/s12862-017-1076-y · Cited by 56 · see citing works
“The matrix was analyzed using equally weighted parsimony in TNT [19] using a heuristic search with 1000 replicates of Wagner trees followed by TBR branch swapping (holding 10 trees per replicate).”
The first specimen of<i>Archaeopteryx</i>from the Upper Jurassic Mörnsheim Formation of Germany
Kundrát, M., Nudds, J., Kear, B. P., Lü, J., & Ahlberg, P. (2019) · Historical Biology · doi:10.1080/08912963.2018.1518443 · Cited by 48 · see citing works
Balanoff, A. M., Smaers, J. B., & Turner, A. H. (2016) · Journal of Anatomy · doi:10.1111/joa.12403 · Cited by 46 · see citing works
A vanished history of skeletonization in Cambrian comb jellies
Ou, Q., Xiao, S., Han, J., Sun, G., Zhang, F., Zhang, Z., & Shu, D. (2015) · Science Advances · doi:10.1126/sciadv.1500092 · Cited by 43 · see citing works
Metamorphosis Is Ancestral for Crown Euarthropods, and Evolved in the Cambrian or Earlier
Wolfe, J. M. (2017) · Integrative and Comparative Biology · doi:10.1093/icb/icx039 · Cited by 35 · see citing works
Evaluating scenarios for the evolutionary assembly of the brachiopod body plan
Murdock, D. J. E., Bengtson, S., Marone, F., Greenwood, J. M., & Donoghue, P. C. J. (2014) · Evolution & Development · doi:10.1111/ede.12059 · Cited by 29 · see citing works
- Authors
- Goloboff, P. A., Farris, J. S., & Nixon, K. C.
- Affiliations
- Consejo Nacional de Investigaciones Científicas y Técnicas (AR)
- Swedish Museum of Natural History (SE)
- Cornell University (US)
- Venue
- Cladistics
- Publisher
- Wiley
- Published
- 2008-09-29
- Volume
- 24
- Issue
- 5
- Pages
- 774-786
- ISSN
- 0748-3007 (ISSN-L)
- 1096-0031
- OpenAlex
- W2151692850
- Cited by
- 5,352
- References
- 36
- Citations by year
- 2026: 107 · 2025: 163 · 2024: 206 · 2023: 223 · 2022: 271 · 2021: 330 · 2020: 344 · 2019: 367 · 2018: 388 · 2017: 428 · 2016: 455 · 2015: 431 · 2014: 434 · 2013: 349 · 2012: 312
- FWCI
- 73.44
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Cladistics (publishedVersion)
- Digital Commons - University of South Florida (University of South Florida) (submittedVersion)
- CONICET Digital (CONICET) (submittedVersion, cc-by-nc-sa)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Diversity and Evolution
- Keywords
- TNT, phylogenetic analysis software, parsimony, continuous characters, discrete characters, character evolution, tree diagrams, scripting languages, phylogenetic simulation
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