leBIBI IV SSU-rDNA (16S) Automated ProKaryotes Phylogeny

DB sources

DB sources

EMBL taxonomy

This is the source of the taxonomy in riboDB and leBIBI

taxonomy

RefSeq and GenBank

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.

Bacteria and Archaea: 16S ribosomal RNA project

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.

DDBJ

LPSN

LPSN for the
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.

LPSN

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

kalign

Mafft

  Katoh, K., & Toh, H. (2008).
Recent developments in the MAFFT multiple sequence alignment program.
  Briefings in bioinformatics, 9(4), 286-298.

MAFFT

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

CIAlign

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.

FastTree

Toytree

  Eaton, D. A. (2020).
  Toytree: A minimalist tree visualization and manipulation library for Python.
  Methods in Ecology and Evolution, 11(1), 187-191.

Toytree

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.

MinVar-Rooting