relative evolutionary divergence (RED) values and median RED values

[Julboteroc]

Dear GTDBTK developers, thank you very much for creating this incredible tool.

I have a question. I used GTDBTK to classify a genome from the Lactobacillaceae family. My genome could not be classified using ANI, so my result was obtained using RED, which yielded 0.95 as it is shown below:

d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g_Limosilactobacillus;s__	N/A	N/A	N/A	N/A	N/A	GCF_001434095.1	95	d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructilactobacillus;s__Fructilactobacillus fructivorans	77.58	0.212	d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructilactobacillus;s__	taxonomic classification defined by topology and ANI	classification based on placement in class-level tree	N/A	95.41	11	0.95171

According to the RED dictionary "red_dictionary.tsv", my median RED value for the taxonomy rank genus is 0.92. Based on these two values, Is my genome within the genus Limosilactobacillus because 0.95 is greater than 0.92, or is it outside the genus Limosilactobacillus because it falls within the RED interval for genus? I understand that similar questions have been asked before, but I'm confused because my result indicates "g__Limosilactobacillus;s__", which means, it could be inside the genus? Thanks in advance

[phugenholtz]

Hi JulianaTk predicts that your sequence is a novel species (because species not assigned in the tax string) in the genus Limosilactobacillus (because the genus is assigned)That’s the easiest way to interpret the output. We always recommend inferring a de novo tree to confirm the Tk result.Bw, PhilSent from my iPhoneOn 26 Jan 2024, at 07:14, Juliana Botero Cardona @.***> wrote: Dear GTDBTK developers, thank you very much for creating this incredible tool. I have a question. I used GTDBTK to classify a genome from the Lactobacillaceae family. My genome could not be classified using ANI, so my result was obtained using RED, which yielded 0.95 as it is shown below:

d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g_Limosilactobacillus;s__ N/A N/A N/A N/A N/A GCF_001434095.1 95 d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructilactobacillus;s__Fructilactobacillus fructivorans 77.58 0.212 d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructilactobacillus;s__ taxonomic classification defined by topology and ANI classification based on placement in class-level tree N/A 95.41 11 0.95171

According to the RED dictionary "red_dictionary.tsv", my median RED value for the taxonomy rank genus is 0.92. Based on these two values, Is my genome within the genus Limosilactobacillus because 0.95 is greater than 0.92, or is it outside the genus Limosilactobacillus because it falls within the RED interval for genus? I understand that similar questions have been asked before, but I'm confused because my result indicates "g__Limosilactobacillus;s__", which means, it could be inside the genus? Thanks in advance

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[Julboteroc]

Dear @phugenholtz , Thank you very much for your reply. In the information provided in summary.txt, it states: "An unassigned species (i.e., s__) indicates that the query genome is either i) placed outside a named genus," which means that the appearance of "g__Limosilactobacillus;s_" does not necessarily mean that it belongs to this genus?

[pchaumeil]

Ticket closed due to inactivity.