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relative evolutionary divergence (RED) values and median RED values #568
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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:
<style>
</style>
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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Dear @phugenholtz , Thank you very much for your reply. |
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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:
<style> </style>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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