T-BAS Citations

If you use T-BAS please cite:

T-BAS v2.3

Carbone, I., White, J. B., Miadlikowska, J., Arnold, A. E., Miller, M. A., Magain, N., U'Ren, J. M. and F. Lutzoni. 2019. T-BAS version 2.1: Tree-Based Alignment Selector toolkit for evolutionary placement of DNA sequences and viewing alignments and specimen metadata on curated and custom trees. ( https://mra.asm.org/content/8/29/e00328-19 ) DOI: 10.1128/mra.00328-19

T-BAS core features

Carbone, I., White, J. B., Miadlikowska, J., Arnold, A. E., Miller, M. A., Kauff, F., U'Ren, J. M., May, G. and F. Lutzoni. 2017. T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads, and metadata visualization; an example with the Pezizomycotina tree of life. Bioinformatics 33: 1160-1168. DOI: 10.1093/bioinformatics/btw808

D3.js

Bostock M, Ogievetsky V, Heer J. D(3): Data-Driven Documents. IEEE Trans Vis Comput Graph. 2011;17(12):2301-9. Epub 2011/10/29. doi: 10.1109/TVCG.2011.185. PubMed PMID: 22034350. https://d3js.org/

If you use the MSAViewer to create a Figure for publication then also cite:

Yachdav, Guy, Sebastian Wilzbach, Benedikt Rauscher, Robert Sheridan, Ian Sillitoe, James Procter, Suzanna E. Lewis, Burkhard Rost, and Tatyana Goldberg. "MSAViewer: interactive JavaScript visualization of multiple sequence alignments." Bioinformatics (2016): btw474. DOI: 10.1093/bioinformatics/btw474

If you use a T-BAS reference tree and metadata please cite:

Pezizomycotina tree

Carbone, I. White, J. B., Miadlikowska, J., Arnold, A. E., Miller, M. A., Kauff, F., U'Ren, J. M., May, G. and F. Lutzoni. 2016. T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads, and metadata visualization: an example with the Pezizomycotina tree of life. Bioinformatics 2016, DOI: 10.1093/bioinformatics/btw808 (https://academic.oup.com/bioinformatics/article/2730230/T-BAS-Tree-Based-Alignment-Selector-toolkit-for) DOI: 10.1093/bioinformatics/btw808

Bacterial tree

Hug, L.A., Baker, B.J., Anantharaman, K., Brown, C.T., Probst, A.J., Castelle, C.J., Butterfield, C.N., Hernsdorf, A.W., Amano, Y., Ise, K., Suzuki, Y., Dudek, N., Relman, D.A., Finstad, K.M., Amundson, R., Thomas, B.C., and Banfield, J.F. 2016. A new view of the tree of life. Nat Microbiol 1:16048. DOI: 10.1038/nmicrobiol.2016.48

Fungal tree

James, T.Y., Kauff, F., Schoch, C.L., Matheny, P.B., Hofstetter, V., Cox, C.J., Celio, G., Gueidan, C., Fraker, E., Miadlikowska, J., Lumbsch, H.T., Rauhut, A., Reeb, V., Arnold, A.E., Amtoft, A., Stajich, J.E., Hosaka, K., Sung, G.H., Johnson, D., O'Rourke, B., Crockett, M., Binder, M., Curtis, J.M., Slot, J.C., Wang, Z., Wilson, A.W., Schussler, A., Longcore, J.E., O'Donnell, K., Mozley-Standridge, S., Porter, D., Letcher, P.M., Powell, M.J., Taylor, J.W., White, M.M., Griffith, G.W., Davies, D.R., Humber, R.A., Morton, J.B., Sugiyama, J., Rossman, A.Y., Rogers, J.D., Pfister, D.H., Hewitt, D., Hansen, K., Hambleton, S., Shoemaker, R.A., Kohlmeyer, J., Volkmann-Kohlmeyer, B., Spotts, R.A., Serdani, M., Crous, P.W., Hughes, K.W., Matsuura, K., Langer, E., Langer, G., Untereiner, W.A., Lucking, R., Budel, B., Geiser, D.M., Aptroot, A., Diederich, P., Schmitt, I., Schultz, M., Yahr, R., Hibbett, D.S., Lutzoni, F., McLaughlin, D.J., Spatafora, J.W., and Vilgalys, R. 2006. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443:818-822. DOI: 10.1038/nature05110

Lecanoromycetes tree

Miadlikowska J, Kauff F, Hofstetter V, Fraker E, Grube M, Hafellner J, Reeb V, Hodkinson BP, Kukwa M, Lucking R et al. . 2006. New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes. Mycologia 98(6):1088-103.

Ramularia tree

Videira SI, Groenewald JZ, Kolecka A, van Haren L, Boekhout T, Crous PW. 2015. Elucidating the Ramularia eucalypti species complex. Persoonia 34:50-64. DOI: 10.3767/003158515x685670

Aspergillus section Flavi tree

Moore, G.G., Olarte, R.A., Horn, B.W., Elliott, J.L., Singh, R., O'Neal, C.J., and Carbone, I. 2017. Global population structure and adaptive evolution of aflatoxin-producing fungi. Ecol Evol 7:9179-9191. DOI: 10.1002/ece3.3464

Fusarium solani species complex tree

O'Donnell, K., Sutton, D.A., Wiederhold, N., Robert, V.A., Crous, P.W., and Geiser, D.M. 2016. Veterinary Fusarioses within the United States. J Clin Microbiol 54:2813-2819 DOI: 10.1128/jcm.01607-16

Xylariaceae tree

U'Ren, J.M., Miadlikowska, J., Zimmerman, N.B., Lutzoni, F., Stajich, J.E., and Arnold, A.E. 2016. Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota). Mol Phylogenet Evol 98:210-232. DOI: 10.1016/j.ympev.2016.02.010

Sebacinales tree

Garnica, S., Riess, K., Schon, M.E., Oberwinkler, F., and Setaro, S.D. 2016. Divergence Times and Phylogenetic Patterns of Sebacinales, a Highly Diverse and Widespread Fungal Lineage. PloS one 11:e0149531. DOI: 10.1371/journal.pone.0149531

Peltigera tree

Chagnon P-L, Magain N, Miadlikowska J, Lutzoni F. 2019. Species diversification and phylogenetically constrained symbiont switching generated high modularity in the lichen genus Peltigera. Journal of Ecology doi:10.1111/1365-2745.13207. DOI: 10.1111/1365-2745.13207

Laboulbeniomycetes tree

Haelewaters D, Pfliegler WP, Gorczak M, Pfister DH. 2019. Birth of an order: Comprehensive molecular phylogenetic study excludes Herpomyces (Fungi, Laboulbeniomycetes) from Laboulbeniales. Mol Phylogenet Evol 133:286-301. DOI: 10.1016/j.ympev.2019.01.007

section Peltidea tree

Miadlikowska, J., Magain, N., Pardo-De la Hoz, C. J., Niu, D., Goward, T., Sérusiaux, E. and Lutzoni, F. 2018. Species in section Peltidea (aphthosa group) of the genus Peltigera remain cryptic after molecular phylogenetic revision. Plant and Fungal Systematics 63:45–64. DOI: 10.2478/pfs-2018-0007

section Peltigera+Retifoveatae tree

Magain, N., Truong, C., Goward, T., Niu, D., Goffinet, B., Sérusiaux, E., Vitikainen, O., Lutzoni, F., and Miadlikowska, J. 2018. Species delimitation at a global scale reveals high species richness with complex biogeography and patterns of symbiont association in Peltigera section Peltigera (lichenized Ascomycota: Lecanoromycetes). Taxon 67:836–870. DOI: 10.12705/675.3

section Chloropeltigera tree

Pardo De la Hoz, C. J., Magain, N., Lutzoni, F., Goward, T., Restrepo, S., and Miadlikowska, J. 2018 Contrasting symbiotic patterns in two closely related lineages of trimembered lichens of the genus Peltigera. Frontiers in Microbiology 9:2770. DOI: 10.3389/fmicb.2018.02770. DOI: 10.3389/fmicb.2018.02770

section Polydactylon tree

Magain, N., Miadlikowska, J., Mueller, O., Gajdeczka, M., Truong, C., Salamov, A., Dubchak, I., Grigoriev, I. V., Goffinet, B., Sérusiaux, E., and Lutzoni, F. 2017. Conserved genomic collinearity as a source of broadly applicable, fast evolving, markers to resolve species complexes: A case study using the lichen-forming genus Peltigera section Polydactylon. 25th anniversary issue of Molecular Phylogenetics and Evolution 117:10–29. DOI: 10.1016/j.ympev.2017.08.013

Archaea tree

Archaea (unpublished)

Aspergillus flavus tree

Bacteria genomic tree

Bacteria original Hug et al tree

Chloropeltigera tree

covid2 tree

covid2 (unpublished)

covid tree

covid (unpublished)

Erysiphe tree

Bradshaw, M., Ivors, K., Broome, J.C., Carbone, I., Braun, U., Yang, S., Meng, E., Warres, B., Cline, W.O., Moparthi, S., Llanos, A.K., Apaza, W., Liu, M., Carey, J., El Ghazouani, M., Carvalho, R., Elliott, M., Boufford, D., Coetzee, T., de Wet, J., Mitchell, J.K., Quijada, L., Meeboon, J., Takamatsu, S., Crouch, U., LaGreca, S. and Pfister, D.H. (2025), An emerging fungal disease is spreading across the globe and affecting the blueberry industry. New Phytol. https://doi.org/10.1111/nph.20351

Fungi 267 tree

Li, Y., J. L. Steenwyk, Y. Chang, Y. Wang, T. Y. James, J. E. Stajich, J. W. Spatafora, M. Groenewald, C. W. Dunn, C. T. Hittinger, X.-X. Shen and A. Rokas (2021). A genome-scale phylogeny of the kingdom Fungi. Current Biology 31(8): 1653-1665.e1655. https://doi.org/10.1016/j.cub.2021.01.074

Fungi v3 tree

Fungi_v3 (unpublished)

Fusarium solani tree

O'Donnell, K., Sutton, D.A., Wiederhold, N., Robert, V.A., Crous, P.W., and Geiser, D.M. 2016. Veterinary Fusarioses within the United States. J Clin Microbiol 54:2813-2819.

Fusarium species complex tree

O’Donnell, K., Cigelnik, E., & Nirenberg, H. I. (1998). Molecular Systematics and Phylogeography of the Gibberella fujikuroi Species Complex. Mycologia, 90(3), 465–493. https://doi.org/10.2307/3761407

Graphideae tree

Medeiros, I., & Lutzoni, F. (2022). Contribution to a modern treatment of Graphidaceae biodiversity in South Africa: Genera of tribe Graphideae with hyaline ascospores. The Lichenologist, 54(5), 253-270. doi:10.1017/S0024282922000263

Helotiales sclerotinioid clade v1 tree

Gómez -Zapata PA, Haelewaters D, Quijada L, Pfister DH, Aime MC. 2021. Notes on Trochila (Ascomycota, Leotiomycetes), with new species and combinations. MycoKeys 78: 21-47. DOI: 10.3897/mycokeys.78.62046

Laboulbeniomycetes v1 tree

Laboulbeniomycetes v2 tree

Blackwell M, Haelewaters D, Pfister DH. 2020. Laboulbeniomycetes: Evolution, natural history, and Thaxter's final word. Mycologia doi:10.1080/00275514.2020.1718442.

Lecanoraceae tree

Medeiros, I.D., Mazur, E., Miadlikowska, J., Flakus, A., Rodriguez-Flakus, P., Pardo-De la Hoz, C.J., Cieślak, E., Śliwa, L., and Lutzoni, F. (2021) Turnover of lecanoroid mycobionts and their Trebouxia photobionts along an elevation gradient in Bolivia highlights the role of environment in structuring the lichen symbiosis. Frontiers in Microbiology 12: 774839. DOI: 10.3389/fmicb.2021.774839

Zhao, X., Leavitt, S.D., Zhao, Z.T., Zhang, L.L., Arup, U., Grube, M., Pérez-Ortega, S., Printzen, C., Śliwa, L., Kraichak, E., Divakar, P.K., Crespo A., and & Lumbsch, H.T. (2016) Towards a revised generic classification of lecanoroid lichens (Lecanoraceae, Ascomycota) based on molecular, morphological and chemical evidence. Fungal Diversity 78: 293–304. DOI: 10.1007/s13225-015-0354-5

Lecanoromycetes v1a tree

Miadlikowska,J. et al. (2006) New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes. Mycologia, 98, 1088–1103.

Lecanoromycetes v1 tree

Lecanoromycetes v2 tree

Leotiomycetes v1 tree

Haelewaters D, Park D, Johnston PR. 2021. Multilocus phylogenetic analysis reveals that Cyttariales is a synonym of Helotiales. Mycological Progress 20: 1323-1330. DOI: 10.1007/s11557-021-01736-2

Life 16 tree

Life3 tree

Bacteria v3 (unpublished)

Nostoc section 2 1 tree

Unpublished

Nostoc section 2 2 tree

Unpublished

Nostoc section 2 4 tree

Unpublished

Nostoc section 3 10 tree

Unpublished

Nostoc section 3 11 tree

Unpublished

Nostoc section 3 12 tree

Unpublished

Nostoc section 3 1 tree

Unpublished

Nostoc section 3 2 tree

Unpublished

Nostoc section 3 4 tree

Unpublished

Nostoc section 3 5 tree

Unpublished

Nostoc section 3 6 tree

Unpublished

Nostoc section 3 7 tree

Unpublished

Nostoc section 3 8 tree

Unpublished

Nostoc section 3 9 tree

Unpublished

Nostoc tree

Unpublished

Passalidae tree

Beza-Beza, C. F.; Jiménez-Ferbans, L.; McKenna, D. D. 2020. Phylogeny and systematics of wood-degrading neotropical bess beetles (Coleoptera: Passalidae: Passalinae). Arthropod Systematics & Phylogeny 78(2), 287 – 308. DOI: 10.26049/ASP78-2-2020-05

Peltidea tree

Peltigera tree

Pezizomycotina v2 1 tree

Pezizomycotina v2.1 (unpublished)

pezizo v1 tree

Carbone, I. White, J. B., Miadlikowska, J., Arnold, A. E., Miller, M. A., Kauff, F., U′Ren, J. M., May, G. and F. Lutzoni. 2016. T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads, and metadata visualization: an example with the Pezizomycotina tree of life. Bioinformatics 2016, doi: 10.1093/bioinformatics/btw808

pezizo v2 1 tree

pezizo v2 1 (unpublished)

pezizo v2 tree

Carbone, I., White, J. B., Miadlikowska, J., Arnold, A. E., Miller, M. A., Magain, N., U'Ren, J. M. and F. Lutzoni. 2019. T-BAS version 2.1: Tree-Based Alignment Selector toolkit for evolutionary placement and viewing of alignments and metadata on curated and custom reference trees. Microbiology Resource Announcements In Review

Phytophthora CoxI 2 tree

Coomber, A., Saville, A., Carbone, I. and J. B. Ristaino. 2023. An open-access T-BAS phylogeny for emerging Phytophthora species. PLoS One 18(4): e0283540. https://doi.org/10.1371/journal.pone.0283540

Phytophthora Micro 2 tree

Phytophthora Nuclear 2 tree

Polydactylon tree

Ramularia tree

Videira SI, Groenewald JZ, Kolecka A, van Haren L, Boekhout T, Crous PW. 2015. Elucidating the Ramularia eucalypti species complex. Persoonia 34:50-64.

Ramularia v1 tree

Videira SI, Groenewald JZ, Kolecka A, van Haren L, Boekhout T, Crous PW. 2015. Elucidating the Ramularia eucalypti species complex. Persoonia 34:50-64. http://dx.doi.org/10.3767/003158515X685670

Rhizoctonia v1 tree

Gonzalez D, Rodriguez-Carres M, Boekhout T, et al. (2016) Phylogenetic relationships of Rhizoctonia fungi within the Cantharellales. Fungal Biol 120, 603-619. DOI: 10.1016/j.funbio.2016.01.012

Rhizoctonia v2 1 tree

Gonzalez D, Rodriguez-Carres M, Boekhout T, et al. (2016) Phylogenetic relationships of Rhizoctonia fungi within the Cantharellales. Fungal Biol 120, 603-619. DOI: 10.1016/j.funbio.2016.01.012

Rhizoctonia v2 tree

Gonzalez D, Rodriguez-Carres M, Boekhout T, et al. (2016) Phylogenetic relationships of Rhizoctonia fungi within the Cantharellales. Fungal Biol 120, 603-619. DOI: 10.1016/j.funbio.2016.01.012

Sebacinales tree

section Peltigera tree

Trebouxia clade A tree

Medeiros, I.D., Mazur, E., Miadlikowska, J., Flakus, A., Rodriguez-Flakus, P., Pardo-De la Hoz, C.J., Cieślak, E., Śliwa, L., and Lutzoni, F. (2021) Turnover of lecanoroid mycobionts and their Trebouxia photobionts along an elevation gradient in Bolivia highlights the role of environment in structuring the lichen symbiosis. Frontiers in Microbiology 12:774839. DOI: 10.3389/fmicb.2021.774839

Muggia, L., Nelsen, M. P., Kirika, P. M., Barreno, E., Beck, A., Lindgren, H., Lumbsch, H.T., Leavitt, S.D., and Trebouxia working group. (2020) Formally described species woefully underrepresent phylogenetic diversity in the common lichen photobiont genus Trebouxia (Trebouxiophyceae, Chlorophyta): an impetus for developing an integrated taxonomy. Molecular Phylogenetics and Evolution 149:106821. DOI: 10.1016/j.ympev.2020.106821

Trebouxia clade C tree

Medeiros, I.D., Mazur, E., Miadlikowska, J., Flakus, A., Rodriguez-Flakus, P., Pardo-De la Hoz, C.J., Cieślak, E., Śliwa, L., and Lutzoni, F. (2021) Turnover of lecanoroid mycobionts and their Trebouxia photobionts along an elevation gradient in Bolivia highlights the role of environment in structuring the lichen symbiosis. Frontiers in Microbiology 12:774839. DOI: 10.3389/fmicb.2021.774839

Muggia, L., Nelsen, M. P., Kirika, P. M., Barreno, E., Beck, A., Lindgren, H., Lumbsch, H.T., Leavitt, S.D., and Trebouxia working group. (2020) Formally described species woefully underrepresent phylogenetic diversity in the common lichen photobiont genus Trebouxia (Trebouxiophyceae, Chlorophyta): an impetus for developing an integrated taxonomy. Molecular Phylogenetics and Evolution 149:106821. DOI: 10.1016/j.ympev.2020.106821

Trebouxia clade I tree

Medeiros, I.D., Mazur, E., Miadlikowska, J., Flakus, A., Rodriguez-Flakus, P., Pardo-De la Hoz, C.J., Cieślak, E., Śliwa, L., and Lutzoni, F. (2021) Turnover of lecanoroid mycobionts and their Trebouxia photobionts along an elevation gradient in Bolivia highlights the role of environment in structuring the lichen symbiosis. Frontiers in Microbiology 12:774839. DOI: 10.3389/fmicb.2021.774839

Muggia, L., Nelsen, M. P., Kirika, P. M., Barreno, E., Beck, A., Lindgren, H., Lumbsch, H.T., Leavitt, S.D., and Trebouxia working group. (2020) Formally described species woefully underrepresent phylogenetic diversity in the common lichen photobiont genus Trebouxia (Trebouxiophyceae, Chlorophyta): an impetus for developing an integrated taxonomy. Molecular Phylogenetics and Evolution 149:106821. DOI: 10.1016/j.ympev.2020.106821

Trebouxia clade S tree

Medeiros, I.D., Mazur, E., Miadlikowska, J., Flakus, A., Rodriguez-Flakus, P., Pardo-De la Hoz, C.J., Cieślak, E., Śliwa, L. and Lutzoni, F. (2021) Turnover of lecanoroid mycobionts and their Trebouxia photobionts along an elevation gradient in Bolivia highlights the role of environment in structuring the lichen symbiosis. Frontiers in Microbiology 12:774839. DOI: 10.3389/fmicb.2021.774839

Muggia, L., Nelsen, M. P., Kirika, P. M., Barreno, E., Beck, A., Lindgren, H., Lumbsch, H.T., Leavitt, S.D., and Trebouxia working group. (2020) Formally described species woefully underrepresent phylogenetic diversity in the common lichen photobiont genus Trebouxia (Trebouxiophyceae, Chlorophyta): an impetus for developing an integrated taxonomy. Molecular Phylogenetics and Evolution 149:106821. DOI: 10.1016/j.ympev.2020.106821

Trebouxia tree

Medeiros, I.D., Mazur, E., Miadlikowska, J., Flakus, A., Rodriguez-Flakus, P., Pardo-De la Hoz, C.J., Cieślak, E., Śliwa, L., and Lutzoni, F. (2021) Turnover of lecanoroid mycobionts and their Trebouxia photobionts along an elevation gradient in Bolivia highlights the role of environment in structuring the lichen symbiosis. Frontiers in Microbiology 12:774839. DOI: 10.3389/fmicb.2021.774839

Muggia, L., Nelsen, M. P., Kirika, P. M., Barreno, E., Beck, A., Lindgren, H., Lumbsch, H.T., Leavitt, S.D., and Trebouxia working group. (2020) Formally described species woefully underrepresent phylogenetic diversity in the common lichen photobiont genus Trebouxia (Trebouxiophyceae, Chlorophyta): an impetus for developing an integrated taxonomy. Molecular Phylogenetics and Evolution 149:106821. DOI: 10.1016/j.ympev.2020.106821