‘The All-Species Living Tree’ Project

A valuable resource particularly for microbial taxonomists

The new ARB software estable version 7.0 has been released!!!

The ARB soft­ware, is a graph­ic­ally ori­ented pack­age com­pris­ing vari­ous tools for se­quence data­base hand­ling and data ana­lysis. With this latest up­date, users now profit from many new fea­tures as well as im­proved sta­bil­ity. For further information and link to ARB download page please visit https://www.mpi-bremen.de/en/ARB-7.html

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_09_2021
LTP database in ARB format LTP_09_2021.arb
LTP database in csv format LTP_09_2021.csv
LTP_all tree in newick format LTP_all_09_2021.ntree
LTP_core tree in newick format LTP_core_09_2021.ntree
LTP_09_2021 Release Notes LTP_09_2021_release_notes.pdf
LTP_09_2021 Supplementary tables LTP_09_2021_release_tables.xlsx
LTP database with aligned sequences in fasta format LTP_09_2021_aligned.fasta
LTP database local blast ncbi database format LTP_09_2021_blastdb.fasta
LTP database in compressed fasta format LTP_09_2021_compressed.fasta
PREVIOUS DOWNLOADS
LTP – 2020
LTP – 2021

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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