Release notes for GTDB R04-RS89

Release date: June 17th, 2019

GTDB R04-RS89 contains 23,458 bacterial and 1,248 archaeal species clusters which
span 145,904 genomes.


MAJOR CHANGES from R03-RS86
---------------------------

- GTDB now uses average nucleotide identity to circumscribe species clusters
- GTDB species clusters are defined by a single representative genome which is
  a genome assembled from the type strain where applicable
- All genomes now have taxonomic assignments from the rank of domain to species
- Archaeal reference tree is now inferred with IQ-Tree v1.6.9 under the PMSF model, 
  a rapid approximation of the C10 mixture model (LG+C10+F+G), using FastTree v2.1.10 
  to infer an initial guide tree
- Bacterial reference tree is now inferred with FastTree v2.1.10 under the WAG model
- Reference trees now contain 1 genome per GTDB species cluster
- Archaeal and bacterial reference trees are now inferred from filtered MSAs that 
  span ~5,000 amino acids selected from the 122 archaeal and 120 bacterial 
  previously used in full for phylogenetic inference
- The taxonomy browser (gtdb.ecogenomic.org/tree) colour highlights type species 
  and type strains


MINOR UPDATES
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August 9, 2019: ar122_r89.tree was updated to contain bootstrap values and to be
                rooted on DPANN