Gene identification
-------------------

- Gene calling was performed with Prodigal v2.6.3 (Hyatt et al., 2010) and marker 
  genes identified and aligned using HMMER v3.1b1 (Eddy, 2011). Marker genes and 
  corresponding HMMs are from the Pfam v27 (Finn et al., 2014) and TIGRFAMs 
  v15.0 (Haft et al., 2003) databases.
  

Tree inference
--------------

- Bacteria reference tree is inferred with FastTree v2.1.10 under the WAG model
  from the concatenated alignment of 120 ubiquitous bacterial genes (Parks et al., 2018)
- Archaea reference tree is inferred with IQ-Tree v1.6.9 under the PMSF model
  from the concatenated alignment of 122 ubiquitous archaeal genes (Parks et al., 2018),
  using FastTree v2.1.10 to infer an initial guide tree


Identifying 16S rRNA sequences
------------------------------

- Sequences are identified using nhmmer v3.1b2 (Wheeler and Eddy, 2013) with the 
  16S rRNA model (RF00177) from the RFAM database (Kalvari et al., 2018).
  
  
Average nucleotide identity
---------------------------

Average nucleotide identity (ANI) and alignment fraction (AF) values were calculated
with FastANI v1.3 (Jain et al., 2018).


Additional information
----------------------

Please consult the following GTDB publications for additional information:

Parks, D. H., et al. (2018). A standardized bacterial taxonomy based on genome 
  phylogeny substantially revises the tree of life. Nature Biotechnology, 
  36: 996-1004.

Parks DH, et al. (2019). Selection of representative genomes for 24,706 bacterial 
  and archaeal species clusters provide a complete genome-based taxonomy. bioRxiv:
  https://doi.org/10.1101/771964

Chaumeil P-A, et al. (2019). GTDB-Tk: a toolkit to classify genomes with the 
  Genome Taxonomy Database. Bioinformatics, btz848:
  https://doi.org/10.1093/bioinformatics/btz848.


REFERENCES
----------

Eddy SR. 2011. Accelerated Profile HMM Searches. PLoS Comput Biol 7: e1002195.

Finn RD, et al. 2014. Pfam: The protein families database. Nucleic Acids Res 
  42: D222-230.
  
Haft DH, Selengut JD, White O. 2003. The TIGRFAMs database of protein families. 
  Nucl Acids Res 31: 371-373.

Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. 2010. 
  Prodigal: Prokaryotic gene recognition and translation initiation site 
  identification. BMC Bioinformatics 11: 119.
  
Jain C, et al. (2018). High throughput ANI analysis of 90K prokaryotic genomes 
  reveals clear species boundaries. Nature Communication 9: 5114.

Kalvari I, et al. 2018. Rfam 13.0: shifting to a genome-centric resource for 
  non-coding RNA families. Nucleic Acids Res. 46(D1):D335-D342.
  
Parks DH, et al. 2017. Recovery of nearly 8,000 metagenome-assembled genomes 
  substantially expands the tree of life. Nat Microbiol 2: 1533-42.

Wheeler TJ, Eddy SR. 2013. nhmmer: DNA homology search with profile HMMs. 
  Bioinformatics. 2013 Oct 1;29(19):2487-9.