If you use T-BAS please cite:
T-BAS v2.1
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. Microbiology Resource Announcements In Review
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
CIPRES REST API
Miller, M.A., Schwartz, T., Pickett, B.E., et al. (2015) A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway. Evolutionary Bioinformatics 11, 43-48.DOI: 10.4137/EBO.S21501 ( https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4362911/ )
If you use a T-BAS reference tree and metadata please cite:
Pezizomycotina reference 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)
Bacterial reference 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.
Fungal reference 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.
Lecanoromycetes reference 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 reference 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.
Aspergillus section Flavi reference 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.
Fusarium solani species complex reference 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
Xylariaceae reference 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.
Sebacinales reference 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.
Rhizoctonia reference tree
Gonzalez D, Rodriguez-Carres M, Boekhout T, et al. (2016) Phylogenetic relationships of Rhizoctonia fungi within the Cantharellales. Fungal Biol 120, 603-619.
Peltigera reference tree
Magain et al. unpublished
Laboulbeniomycetes reference 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.