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donovan-h-parks / PhyloRank

Assign taxonomic ranks based on evolutionary divergence.
GNU General Public License v3.0
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AAI vs RED #17

Open cruizperez opened 3 years ago

cruizperez commented 3 years ago

Hello, I was using GTDBtk to classify several genomes and found a file with RED values for pairs of genomes in the dabatase used, which I assumed was calculated from the Bac120 tree (and confirmed using PhyloRank). I have a question about RED values in general, is the comparison of RED values vs genome relatedness (AAI) values a fair comparison, can one classify genomes solely based on RED values, or this metric is more to be used in combination with phylogenetic placement only? Thanks for the tool!

donovan-h-parks commented 3 years ago

Hi. The GTDB classification framework is based on RED values. RED is only moderately correlated with AAI. The major difference being that RED considers relative rates of evolution whereas AAI does not (i.e. fast evolving groups will have high AAI even if they diverged relatively recently).