List of phylogenetics software (English Wikipedia)

Ray S, Jia B, Safavi S, Opijnen T, Isberg R, Rosch J, Bento J. Exact inference under the perfect phylogeny model. arXiv:1908.08623.
Hellmuth M, Wieseke N, Lechner M, Lenhof HP, Middendorf M, Stadler PF (February 2015). "Phylogenomics with paralogs". Proceedings of the National Academy of Sciences of the United States of America. 112 (7): 2058–63. arXiv:1712.06442. Bibcode:2015PNAS..112.2058H. doi:10.1073/pnas.1412770112. PMC 4343152. PMID 25646426.
Samson, Stéphane; Lord, Étienne; Makarenkov, Vladimir (26 May 2022). "SimPlot++: a Python application for representing sequence similarity and detecting recombination". Bioinformatics. 38 (11): 3118–3120. arXiv:2112.09755. doi:10.1093/bioinformatics/btac287. PMID 35451456.

cibiv.at

"IQPNNI - Important Quartet Puzzling and Nearest Neighbor Interchange". Wien, Austria: University of Vienna. 20 August 2010. Retrieved 5 February 2025.

doi.org

eurekaselect.com

github.com

"iqtree2". Retrieved 5 February 2025.

handle.net

harvard.edu

Lord E, Leclercq M, Boc A, Diallo AB, Makarenkov V (2012). "Armadillo 1.1: an original workflow platform for designing and conducting phylogenetic analysis and simulations". PLOS One. 7 (1): e29903. Bibcode:2012PLoSO...729903L. doi:10.1371/journal.pone.0029903. PMC 3256230. PMID 22253821.
Jiang Y, Qiu Y, Minn AJ, Zhang NR (September 2016). "Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing". Proceedings of the National Academy of Sciences of the United States of America. 113 (37): E5528-37. Bibcode:2016PNAS..113E5528J. doi:10.1073/pnas.1522203113. PMC 5027458. PMID 27573852.
Price MN, Dehal PS, Arkin AP (March 2010). "FastTree 2--approximately maximum-likelihood trees for large alignments". PLOS One. 5 (3): e9490. Bibcode:2010PLoSO...5.9490P. doi:10.1371/journal.pone.0009490. PMC 2835736. PMID 20224823.
Campbell, Ellsworth M.; Boyles, Anthony; Shankar, Anupama; Kim, Jay; Knyazev, Sergey; Cintron, Roxana; Switzer, William M. (2021-09-07). "MicrobeTrace: Retooling molecular epidemiology for rapid public health response". PLOS Computational Biology. 17 (9): e1009300. Bibcode:2021PLSCB..17E9300C. doi:10.1371/journal.pcbi.1009300. ISSN 1553-7358. PMC 8491948. PMID 34492010.
Hellmuth M, Wieseke N, Lechner M, Lenhof HP, Middendorf M, Stadler PF (February 2015). "Phylogenomics with paralogs". Proceedings of the National Academy of Sciences of the United States of America. 112 (7): 2058–63. arXiv:1712.06442. Bibcode:2015PNAS..112.2058H. doi:10.1073/pnas.1412770112. PMC 4343152. PMID 25646426.
Thomas, Gavin H.; Hartmann, Klaas; Jetz, Walter; Joy, Jeffrey B.; Mimoto, Aki; Mooers, Arne O. (2013). "PASTIS: an R package to facilitate phylogenetic assembly with soft taxonomic inferences". Methods in Ecology and Evolution. 4 (11): 1011–1017. Bibcode:2013MEcEv...4.1011T. doi:10.1111/2041-210X.12117. ISSN 2041-210X. S2CID 86694418.
Arenas, Miguel; Bastolla, Ugo (2020). "ProtASR2: Ancestral reconstruction of protein sequences accounting for folding stability". Methods in Ecology and Evolution. 11 (2): 248–257. Bibcode:2020MEcEv..11..248A. doi:10.1111/2041-210X.13341. ISSN 2041-210X.

nih.gov

oup.com

rdg.ac.uk

retractionwatch.com

semanticscholar.org

Thind, Amarinder Singh; Sinha, Somdatta (2023). "Using Chaos-Game-Representation for Analysing the SARS-CoV-2 Lineages, Newly Emerging Strains and Recombinants". Current Genomics. 24 (3): 187–195. doi:10.2174/0113892029264990231013112156. PMC 10761335. PMID 38178984. S2CID 264500732.
Thompson, Julie D.; Gibson, Toby J.; Higgins, Des G. (August 2002). "Multiple sequence alignment using ClustalW and ClustalX". Current Protocols in Bioinformatics. Chapter 2: 2.3.1–2.3.22. doi:10.1002/0471250953.bi0203s00. ISSN 1934-340X. PMID 18792934. S2CID 34156490.
Criscuolo A (June 2019). "A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies". Research Ideas and Outcomes. 5: e36178. doi:10.3897/rio.5.e36178. S2CID 196180156.
O'Leary, Maureen A.; Kaufman, Seth (October 2011). "MorphoBank: phylophenomics in the "cloud"". Cladistics. 27 (5): 529–537. doi:10.1111/j.1096-0031.2011.00355.x. PMID 34875801. S2CID 76652345.
Thomas, Gavin H.; Hartmann, Klaas; Jetz, Walter; Joy, Jeffrey B.; Mimoto, Aki; Mooers, Arne O. (2013). "PASTIS: an R package to facilitate phylogenetic assembly with soft taxonomic inferences". Methods in Ecology and Evolution. 4 (11): 1011–1017. Bibcode:2013MEcEv...4.1011T. doi:10.1111/2041-210X.12117. ISSN 2041-210X. S2CID 86694418.

wiley.com

Goloboff, Pablo A.; Farris, James S.; Nixon, Kevin C. (29 September 2008). "TNT, a free program for phylogenetic analysis". Cladistics. 24 (5): 774–786. doi:10.1111/j.1096-0031.2008.00217.x.

worldcat.org

Thompson, Julie D.; Gibson, Toby J.; Higgins, Des G. (August 2002). "Multiple sequence alignment using ClustalW and ClustalX". Current Protocols in Bioinformatics. Chapter 2: 2.3.1–2.3.22. doi:10.1002/0471250953.bi0203s00. ISSN 1934-340X. PMID 18792934. S2CID 34156490.
Fletcher, William; Yang, Ziheng (2009-08-01). "INDELible: A Flexible Simulator of Biological Sequence Evolution". Molecular Biology and Evolution. 26 (8): 1879–1888. doi:10.1093/molbev/msp098. ISSN 0737-4038. PMC 2712615. PMID 19423664.
Minh, Bui Quang; Schmidt, Heiko A; Chernomor, Olga; Schrempf, Dominik; Woodhams, Michael D; von Haeseler, Arndt; Lanfear, Robert (February 2020). "IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era". Molecular Biology and Evolution. 37 (5): 1530–1534. doi:10.1093/molbev/msaa015. ISSN 0737-4038.
Campbell, Ellsworth M.; Boyles, Anthony; Shankar, Anupama; Kim, Jay; Knyazev, Sergey; Cintron, Roxana; Switzer, William M. (2021-09-07). "MicrobeTrace: Retooling molecular epidemiology for rapid public health response". PLOS Computational Biology. 17 (9): e1009300. Bibcode:2021PLSCB..17E9300C. doi:10.1371/journal.pcbi.1009300. ISSN 1553-7358. PMC 8491948. PMID 34492010.
Haschka, Thomas; Ponger, Loic; Escudé, Christophe; Mozziconacci, Julien (2021-06-08). "MNHN-Tree-Tools: a toolbox for tree inference using multi-scale clustering of a set of sequences". Bioinformatics. 37 (21): 3947–3949. doi:10.1093/bioinformatics/btab430. ISSN 1367-4803. PMID 34100911.
Huelsenbeck, J. P.; Ronquist, F. (August 2001). "MRBAYES: Bayesian inference of phylogenetic trees". Bioinformatics. 17 (8): 754–755. doi:10.1093/bioinformatics/17.8.754. ISSN 1367-4803. PMID 11524383.
Yang, Ziheng (May 2007). "PAML 4: Phylogenetic Analysis by Maximum Likelihood". Molecular Biology and Evolution. 24 (8): 1586–1591. doi:10.1093/molbev/msm088. ISSN 0737-4038.
Lanfear, Robert; Frandsen, Paul B; Wright, April M; Senfeld, Tereza; Calcott, Brett (24 December 2016). "PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses". Molecular Biology and Evolution. 34 (3): 772–773. doi:10.1093/molbev/msw260. ISSN 0737-4038.
Thomas, Gavin H.; Hartmann, Klaas; Jetz, Walter; Joy, Jeffrey B.; Mimoto, Aki; Mooers, Arne O. (2013). "PASTIS: an R package to facilitate phylogenetic assembly with soft taxonomic inferences". Methods in Ecology and Evolution. 4 (11): 1011–1017. Bibcode:2013MEcEv...4.1011T. doi:10.1111/2041-210X.12117. ISSN 2041-210X. S2CID 86694418.
Guindon, Stéphane; Dufayard, Jean-François; Lefort, Vincent; Anisimova, Maria; Hordijk, Wim; Gascuel, Olivier (2010-03-29). "New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0". Systematic Biology. 59 (3): 307–321. doi:10.1093/sysbio/syq010. hdl:20.500.11850/25281. ISSN 1076-836X. PMID 20525638.
Arenas, Miguel; Bastolla, Ugo (2020). "ProtASR2: Ancestral reconstruction of protein sequences accounting for folding stability". Methods in Ecology and Evolution. 11 (2): 248–257. Bibcode:2020MEcEv..11..248A. doi:10.1111/2041-210X.13341. ISSN 2041-210X.
Arenas, Miguel (2021-08-27). "ProteinEvolverABC: coestimation of recombination and substitution rates in protein sequences by approximate Bayesian computation". Bioinformatics. 38 (1): 58–64. doi:10.1093/bioinformatics/btab617. ISSN 1367-4803. PMC 8696103. PMID 34450622.
Ferreiro, David; Branco, Catarina; Arenas, Miguel. "Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation". Bioinformatics. 40 (3): btae096. doi:10.1093/bioinformatics/btae096. ISSN 1367-4811. PMC 10914458. PMID 38374231.
Currat, Mathias; Arenas, Miguel; Quilodràn, Claudio S; Excoffier, Laurent; Ray, Nicolas (2019-05-11). "SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal". Bioinformatics. 35 (21): 4480–4483. doi:10.1093/bioinformatics/btz311. ISSN 1367-4803. PMC 6821363. PMID 31077292.
Piñeiro, César; Abuín, José M; Pichel, Juan C (2020-11-01). Ponty, Yann (ed.). "Very Fast Tree: speeding up the estimation of phylogenies for large alignments through parallelization and vectorization strategies". Bioinformatics. 36 (17): 4658–4659. doi:10.1093/bioinformatics/btaa582. ISSN 1367-4803. PMID 32573652.

List of phylogenetics software (English Wikipedia)

arxiv.org

cibiv.at

doi.org

eurekaselect.com

github.com

handle.net

hdl.handle.net

harvard.edu

ui.adsabs.harvard.edu

nih.gov

pubmed.ncbi.nlm.nih.gov

ncbi.nlm.nih.gov

oup.com

academic.oup.com

rdg.ac.uk

evolution.rdg.ac.uk

retractionwatch.com

semanticscholar.org

api.semanticscholar.org

wiley.com

besjournals.onlinelibrary.wiley.com

onlinelibrary.wiley.com

worldcat.org

search.worldcat.org