Visualization of a rooted phylogenetic network

Please type in the code of the phylogenetic network you would like to visualize, as a list of arcs, one arc on each line, with the name of the first vertex (a sequence of digits and/or letters) followed by a whitespace (or anything containing neither digits nor letters), followed by the name of the second vertex (also a sequence of digits and/or letters).
After you click the "Submit" button, this website will use GraphViz to draw it for you!

This collection of networks is also used in this tool which checks which classes of phylogenetic networks they belong to. The data is provided as a set of arc list files in the dataset available at https://doi.org/10.57745/VIW7B2. The code is available under the MIT license at https://github.com/PhilippeGambette/networkDraw

50a 26
50a 24
A51 46
A51 43
52 8
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57 22
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70 55
71 A51
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80 1
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113 33
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120 0
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148 64
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150 34
151 91
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158 61
158 152
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161 88
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171 73
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Examples

You can load examples of 28 phylogenetic networks found in the literature:

Figure 7 of Zhang L., Abhari N., Colijn C., Wu Y. (2023). A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings. Genome Research 33:1053–1060 → load this network!
Figure 5b of Wheeler, W., Washburn, A. (2023). Parsimony optimization of phylogenetic networks. Cladistics 39:456–474 → load this network!
Figure 3.4 at page 99 of Willems, M. (2018). Nouveaux algorithmes pour l'inférence de réseaux phylogénétiques. Phd thesis presented at UQAM (Université du Québec à Montréal) → load this network!
Figure 4.6 at page 139 of Willems, M. (2018). Nouveaux algorithmes pour l'inférence de réseaux phylogénétiques. Phd thesis presented at UQAM (Université du Québec à Montréal) → load this network!
Figure 1 of Wu, D.-D. et al. (2018). Pervasive introgression facilitated domestication and adaptation in the Bos species complex. Nature Ecology & Evolution 2:1139–1145 → load this network!
Figure 4 of Glemin, S., Scornavacca, C., Dainat, J., Burgarella, C., Viader, V., Ardisson, M., Sarah, G., Santoni, S., David, J. & Ranwez, V. (2018). Pervasive hybridizations in the history of wheat relatives. bioRXiv manuscript → load this network!
Figure 4 of Oldman, J., Wu, T., van Iersel, L. & Moulton, V. (2016). TriLoNet: Piecing Together Small Networks to Reconstruct Reticulate Evolutionary Histories. Molecular Biology and Evolution 33(8)1:2151–2162 → load this network!
Figure 3 of Mallick, S. et al. (2016). The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature 538(7624):201–206 → load this network!
Figure 10 of Solís-Lemus, C. & Ané, C. (2016). Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting. PLoS Genetics 12(3):e1005896 → load this network!
Figure 7 of Yu Y., Jermaine C. & Nakhleh L. (2016). Exploring phylogenetic hypotheses via Gibbs sampling on evolutionary networks. BMC Genomics 17:3099 → load this network!
Figure 6 of Wen, D., Yu, Y., Hahn, M. W. & Nakhleh, L. (2016). Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis. Molecular Ecology 25(11):2361-2372 → load this network!
Figure 1 of Lake J. A., Larsen J., Sarna B., de la Haba R. R., Pu Y., Koo H. M., Zhao J. & Sinsheimer J. S. (2016). Rings Reconcile Genotypic and Phenotypic Evolution within the Proteobacteria. Genome Biology and Evolution 7(12):3434-3442 → load this network!
Figure 7 of Szöllősi, G. J., Davín, A. A., Tannier, E., Daubin, V., & Boussau, B. (2015). Genome-scale phylogenetic analysis finds extensive gene transfer among fungi. Phil. Trans. R. Soc. B 370(1678):20140335 → load this network!
Figure 2 of Skoglund, P., Mallick, S., Bortolini, M. C., Chennagiri, N., Hünemeier, T., Petzl-Erler, M. L., ... & Reich, D. (2015). Genetic evidence for two founding populations of the Americas. Nature 525(7567):104-108 → load this network!
Figure 1C of Fontaine, M. C. et al. (2015). Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science 347(6217) → load this network!
Figure 6 of Qin, P. & Stoneking, M. (2015). Denisovan ancestry in East Eurasian and Native American populations. Molecular Biology and Evolution 32:2665-2674 → load this network!
Figure 2 of Raghavan, M., Skoglund, P., Graf, K. E., Metspalu, M., Albrechtsen, A., Moltke, I., ... & Karmin, M. (2014). Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature, 505(7481), 87-91 → load this network!
Figure from The Genealogical World of Phylogenetic Networks, derived from Marcussen, T., Sandve, S. R., Heier, L., Spannagl, M., Pfeifer, M., Jakobsen, K. S., ... & Rogers, J. (2014). Ancient hybridizations among the ancestral genomes of bread wheat. Science 345(6194):1250092 → load this network!
Figure 15 from Willems, M., Tahiri, N. & Makarenkov, V. (2014). A new efficient algorithm for inferring explicit hybridization networks following the Neighbor-Joining principle. Journal of Bioinformatics and Computational Biology 12(05):1450024.1-27 → load this network!
Figure 8 of Prüfer, K., Racimo, F., Patterson, N., Jay, F., Sankararaman, S., Sawyer, S., ... & Li, H. (2014). The complete genome sequence of a Neanderthal from the Altai Mountains. Nature, 505(7481), 43-49 → load this network!
Figure 4 of Unmack, P. J., Dowling, T. E., Laitinen, N. L., Secor, C. L., Mayden, R. L., Shiozawa, D. K, Smith, G. R. (2014). Influence of Introgression and Geological Processes on Phylogenetic Relationships of Western North American Mountain Suckers (Pantosteus, Catostomidae). PLoS ONE 9(3):e90061 → load this network!
Figure 5 of Kannan L. & Wheeler WC (2014). Exactly Computing the Parsimony Scores on Phylogenetic Networks Using Dynamic Programming. Journal of Computational Biology 21(4):303–319 → load this network!
Figure 3 of Lazaridis I et al. (2014). Ancient human genomes suggest three ancestral populations for present-day Europeans, Nature 513:409-413 → load this network!
Figure 2 of von Zabern I, Wagner FF, Moulds JM, Moulds JJ & Flegel WA (2013). D category IV: a group of clinically relevant and phylogenetically diverse partial D. Transfusion 53:2960–2973 → load this network!
Figure 2 of Jenkins P. A., Song Y. S. & Brem R. B. (2012). Genealogy-Based Methods for Inference of Historical Recombination and Gene Flow and Their Application in Saccharomyces cerevisiae. PLoS ONE 7(11):e46947 → load this network!
Figure 5 of Sessa, E. B., Zimmer, E. A. & Givnish, T. J. (2012). Unraveling reticulate evolution in North American Dryopteris (Dryopteridaceae). BMC Evolutionary Biology 12:104 → load this network!
Figure 4 of Marcussen, T., Jakobsen, K.S., Danihelka, J., Ballard, H. E., Blaxland K., Brysting, A. K. & Oxelman, B. (2012). Inferring Species Networks from Gene Trees in High-Polyploid North American and Hawaiian Violets (Viola, Violaceae). Systematic Biology 61(1):107-126 → load this network!
Figure 3 of Reich, D. et al. (2011). Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. The American Journal of Human Genetics 89(4):516-528 → load this network!
Figure 6 of Richards T. A., Soanes D. M., Foster P. G., Leonard G., Thornton C. R. & Talbot N. J. (2009). Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient Horizontal Gene Transfer between Plants and Fungi. The Plant Cell 21(7):1897-1911 → load this network!
Figure 3 of Charlton, N. D., Carbone, I., Tavantzis, S. M. & Cubeta, M. A. (2008). Phylogenetic relatedness of the M2 double-stranded RNA in Rhizoctonia fungi. Mycologia 100(4):555-564 → load this network!
Figure 4 of Koblmüller, S., Duftner, N., Sefc, K. M., Aibara, M., Stipacek, M., Blanc, M., Egger B., Sturmbauer, C. (2007). Reticulate phylogeny of gastropod-shell-breeding cichlids from Lake Tanganyika – the result of repeated introgressive hybridization. BMC Evolutionary Biology 7(7) → load this network!
Figure 5 of Westenberger, S. J., Barnabé, C., Campbell, D. A. & Sturm, N. R. (2005). Two Hybridization Events Define the Population Structure of Trypanosoma cruzi. Genetics 171(2):527-543 → load this network!
Figure 4 of Ge, S., To, S. & Lu, B. R. (1999). Phylogeny of rice genomes with emphasis on origins of allotetraploid species. PNAS 96(25):14400-14405 → load this network!
Figure 56 of Grant, V. (1971). Plant Speciation, Columbia University Press → load this network!
Figure 14.1 of Alston, R. E. & Turner, B. L. (1963). Biochemical systematics, Englewood Cliffs, N.J., Prentice-Hall → load this network!
Figure 5 of Grant, V. (1953). The Role of Hybridization in the Evolution of the Leafty-Stemmed Gilias, Brittonia 5(4):337-367 → load this network!
Figure 96 of Taylor, H. (1945). Cyto-Taxonomy and Phylogeny of the Oleaceae, Evolution 7(1):51-64 → load this network!

The figures extracted from the article cited above are available below: click directly on them to load the corresponding network in the form above!

About this website

This website was started in 2015 during a Merlion Project between Université Paris-Est Marne-la-Vallée and National University of Singapore, involving Philippe Gambette, Andreas Gunawan, Anthony Labarre, Stéphane Vialette and Louxin Zhang.

S. Nguyen and A. Sirunyan added some phylogenetic networks to this website in the context of their Science Académie internship at LIGM in April 2016, as well as Gabriel Schneider during his internship at LIGM in December 2023. Data available under the Etalab Open License 2.0 at https://doi.org/10.57745/VIW7B2, code available under the MIT license at https://github.com/PhilippeGambette/networkDraw.

Contact: Philippe Gambette