DB sources
RNAcentral
RNA central is the main source of the sequences
URS Id link from the result tree
RNAcentral: a hub of information for non-coding RNA sequences.
Nucleic acids research,
2019, vol. 47, no D1, p. D221-D229.
RNAcentral: an international database of ncRNA sequences.
Nucleic acids research,
2015, vol. 43, no D1, p. D123-D129.
RefSeq
RefSeq is the source of the Type Material high quality sequences
O'Leary, N. A., Wright, M. W., Brister, J. R., Ciufo, S., Haddad, D., McVeigh, R.et Al.. (2016).
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic acids research,
44(D1), D733-D745.
LPSN
LPSN is the source of the information concerning the Type Strain status
Species name link from the result tree
Parte, A. C., Carbasse, J. S., Meier-Kolthoff, J. P., Reimer, L. C., & Goeker, M. (2020).
List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. International journal of systematic and evolutionary microbiology,
70(11), 5607.
ACNUC
ACNUC (GenBank) is used to verify the current taxonomy of some sequences wrongly identified in RNAcentral
Gouy, M., & Delmotte, S. (2008). Remote access to ACNUC nucleotide and protein sequence databases at PBIL.
Biochimie,
90(4), 555-562.
DDBJ
Acces to the taxonomy browser from the result tree
Ogasawara, O., Kodama, Y., Mashima, J., Kosuge, T., & Fujisawa, T. (2020).
DDBJ Database updates and computational infrastructure enhancement.
Nucleic acids research, 48(D1), D45-D50.
The programs used by BIBI IV
Exemple of information given with the results

BLAST NCBI
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990).
Basic local alignment search tool.
Journal of molecular biology, 215(3), 403-410.
Camacho, C., Coulouris, G., & Ma, V. A. N. J. Papadopouloset al., 2009
BLAST+: architecture and applications.
BMC bioinformatics, 10(1), 421.
Kalign
Lassmann, T. (2020).
Kalign 3: multiple sequence alignment of large datasets. (2020)
Bioinformatics, Volume 36, Issue 6, 15, 1928–1929,
https://doi.org/10.1093/bioinformatics/btz795
Mafft
Katoh, K., & Toh, H. (2008).
Recent developments in the MAFFT multiple sequence alignment program.
Briefings in bioinformatics, 9(4), 286-298.
Gblocks
Talavera, G., & Castresana, J. (2007).
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments.
Systematic biology, 56(4), 564-577.
CIAlign
CIAlign - A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments
Charlotte Tumescheit, Andrew E. Firth, Katherine Brown
bioRxiv 2020.09.14.291484; doi: https://doi.org/10.1101/2020.09.14.291484
FastTree
Price, M. N., Dehal, P. S., & Arkin, A. P. (2010).
FastTree 2–approximately maximum-likelihood trees for large alignments.
PloS one, 5(3), e9490.
Toytree
Eaton, D. A. (2020).
Toytree: A minimalist tree visualization and manipulation library for Python.
Methods in Ecology and Evolution, 11(1), 187-191.
MinVar-Rooting
Mai, U., Sayyari, E., & Mirarab, S. (2017).
Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction.
PloS one, 12(8), e0182238.