If you use T-BAS 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.
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.
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
(
http://www.la-press.com
)