‘The All-Species Living Tree’ Project

A valuable resource particularly for microbial taxonomists

The LTP

LTP stands for “The All-Species Living Tree» Project that was initiated in 2007 as a joint effort between the Marine Microbiology Group at the IMEDEA, the Molecular Ecology Group at the MPI, the Department of Microbiology of the TUM and with the especial support of Elsevier, publisher of the journal Systematic and Applied Microbiology. The aim of the project was to generate a highly curated database of all available 16S rRNA gene sequences of type strains of Bacteria and Archaea, as well as to reconstruct the most robust phylogenies using the universal alignment implemented in ARB. Along the almost 15 years collaboration, the LTP has been regularly updated to offer the best tool for genealogical reconstructions for taxonomic purposes.

The current release LTP_2020 (Ludwig et al., 2021) introduces important changes over the former as a large set of sequences had been substituted, the universal alignment has been thoroughly improved to accommodate the new sequences that contain insertions, as well to improve the helix structures, and has increased from 42,283 to 98,863 homologous positions. We also provide the most robust phylogenetic tree currently achievable with the available dataset.

Our aim is to regularly improve and update the database. Therefore, the team will acknowledge the help of users notifying some mistakes or gaps that they may find.

To get updated on the news or changes in the LTP release, please add your email here and will be added to the LTP distribution list. In addition, if you want to contact the members of the team, just send us an email to: ltp@imedea.uib-csic.es

  • LTP TEAM

  • COLLABORATORS

Downloads

The new LTP publication can be downloaded for free (until December) here:

Ludwig, W., Viver, T., Westram, R., Gago, J.F., Bustos-Caparros, E., Knittel, K., Amann, R., Rossello-Mora, R. (2021) Release LTP_12_2020, featuring a new ARB alignment and improved 16S rRNA tree for prokaryotic type strains. Syst Appl Microbiol 40: 126218

https://doi.org/10.1016/j.syapm.2021.126218

LTP database  ltp_12_2020.arb
ltp_all tree in newick format  ltp_all.ntree
ltp_all tree in PDF format  tree_ltp_all.pdf
ltp_core tree in newick format  ltp_core.ntree
ltp_core tree in PDF format  tree_ltp_core.pdf
LTP database in aligned sequences in FASTA format  ltp_12_2020_aligned.fasta
LTP database in local blast ncbi dabase format  ltp_12_2020_blastdb.fasta
LTP database in FASTA compressed format  ltp_12_2020_compressed.fasta

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    LTP Publications

    • Yarza, P., M. Richter, J. Peplies, J. Euzeby, R. Amann, K. H. Schleifer, W. Ludwig, F. O. Glöckner, and R. Rossello-Mora. 2008. The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31:241-250. doi:10.1016/j.syapm.2008.07.001

      Link

    • Yarza, P., W. Ludwig, J. Euzeby, R. Amann, K. H. Schleifer, F. O. Glöckner, and R. Rossello-Mora. 2010. Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses. Syst Appl Microbiol 33:291-299. doi:10.1016/j.syapm.2010.08.001

      Link

    • Munoz, R., P. Yarza, W. Ludwig, J. Euzéby, R. Amann, K.H. Schleifer, F.O. Glöckner, and R. Rosselló-Móra. 2011. Release LTPs104 of the All-Species Living Tree. Syst Appl Microbiol 34:169-170. doi:10.1016/j.syapm.2011.03.001

      Link

    • Ludwig, W., Viver, T., Westram, R., Gago, J.F., Bustos-Caparros, E., Knittel, K., Amann, R., Rossello-Mora, R. (2021) Release LTP_12_2020, featuring a new ARB alignment and improved 16S rRNA tree for prokaryotic type strains. Syst Appl Microbiol 40: 126218

      Link