The use of PhyloRNA is free of charge. The authors have taken all necessary steps to ensure that the database and website are implemented correctly and perform their intended function as described in the documentation. However, neither the authors nor the University of Camerino guarantee accuracy, suitability for a particular purpose, or the continued availability of PhyloRNA.
PhyloRNA currently consists of RNA secondary structures from various sources. For each RNA sequence, we provide the corresponding BPSEQ file, FASTA file, dot-bracket (DB) file, and CT file. All files are available for download after a search. Additionally, a CSV file is provided, containing complete information, including phylogeny, about each downloaded RNA secondary structure.
The first version of PhyloRNA went online in December 2025.
The phylogeny information provided by SILVA, ENA, LTP, NCBI, and GTDB was updated as of December 2025.
Future updates are scheduled every six months and will be reported on this page.
RCSB Protein Data Bank: https://www.rcsb.org/
Gutell Lab CRW Site: https://crw-site.chemistry.gatech.edu/
CRW2: Comparative RNA Web-2https://crw-site.chemistry.gatech.edu/
tmRNA Database: https://rth.dk/resources/rnp/tmRDB/tmRDB.html
SRP Database: https://rth.dk/resources/rnp/SRPDB/
Additionally, we request that you cite the appropriate publications listed below as well as the original sources of the PhyloRNA data that you used, which are stated above.
[PDB] Westbrook J, Feng Z, Chen L, Yang H, Berman H: The Protein Data Bank and structural genomics. Nucleic Acids Res 2003, 31:489-491.
[CRW] Cannone J, Subramanian S, Schnare M, Collett J, D'Souza L, Du Y, Feng B, Lin N, Madabusi L, Muller K, Pande N, Shang Z, Yu N, Gutell R: The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 2002, 3:2. [Correction: BMC Bioinformatics 3:15.]
[CRW2]Chan C.X., Burrell N.E., Zirbel C.L., Lee J.C., Jeon Y., Adams A., Gutell R.R. (2023). The Comparative RNA Web (CRW) Site – version 2: a database of covariation-based secondary structures. Manuscript in preparation.
[tmRDB,SRPDB] Andersen ES, Rosenblad MA, Larsen N, Westergaard JC, Burks J, Wower IK, Wower J, Gorodkin J, Samuelsson T, Zwieb C: The tmRDB and SRPDB resources. Nucleic Acids Res 2006, 34(Database issue):163-168.
[SILVA] Source: arb-silva, https://www.arb-silva.de/ used under a Creative Commons Attribution 4.0 International Public License (https://creativecommons.org/licenses/by/4.0/legalcode)
[SILVA] Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research 41:D590-D596
[SILVA] Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T,Peplies J, Ludwig W, Glockner FO (2014) The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Nucleic Acid Res. 42:D643-D648
[LTP] Source: mmg-ltp, https://imedea.uib-csic.es/mmg/ltp/
[GTDB] Source: gtdb, https://gtdb.ecogenomic.org/
[GTDB] Parks, D.H., et al. (2021). "GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy." Nucleic Acids Research, https://doi.org/10.1093/nar/gkab776
[GTDB] Rinke, C, et al. (2021). "A standardized archaeal taxonomy for the Genome Taxonomy Database Nature Microbiology 6, 946–959 (2021). https://doi.org/10.1038/s41564-021-00918-8