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title: Example for Jen
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# Summary
* Wanted to know how many reference genomes of the *Rubrobacter* genus available in NCBI were capable of carbon fixation
* At the time of searching (30-Mar-2021), NCBI had 46 assemblies of *Rubrobacter*
* After seeing a phylogenomic tree of them, and taxonomically classifying them with the current gold standard in bacterial/archaeal taxonomy, the [Genome Taxonomy Database (GTDB)](https://gtdb.ecogenomic.org/), the top 8 in the tree below in their own clade are better taxonomically classified as belonging to the phylum Chloroflexota


<a href="https://i.imgur.com/6q9fuYl.png"><img src="https://i.imgur.com/6q9fuYl.png"></a>

<a href="https://i.imgur.com/Ebr1lsQ.png"><img src="https://i.imgur.com/Ebr1lsQ.png"></a>

[Interactive tree here](https://itol.embl.de/tree/1566850116437001616542516)

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It's important to note that NCBI very clearly states it is not an authoritative source on classification on every taxonomy page, e.g. bottom of *Rubrobacter* tax page [here](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=42255&lvl=3&lin=f&keep=1&srchmode=1&unlock)

> *Disclaimer: The NCBI taxonomy database is not an authoritative source for nomenclature or classification - please consult the relevant scientific literature for the most reliable information.*

So it's not "wrong", it just isn't a database dedicated to bacterial/archaeal taxonomy, it's busy doing everything else in the world 🙂

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# Accessions for all 46 *Rubrobacter* in NCBI, and their GTDB taxonomy

```
user_genome      classification
GCA_013695915.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_A;s__
GCA_016781585.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_A;s__
GCA_016781605.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_A;s__
GCA_016781625.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_A;s__
GCA_016781675.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_A;s__
GCA_016781705.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_A;s__
GCA_016781775.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_A;s__
GCA_016781805.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_A;s__
GCF_011492965.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_A;s__
VAL_D01-MAG-140  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_A;s__
GCF_001029505.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_A;s__Rubrobacter_A aplysinae
GCF_000014185.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_B;s__Rubrobacter_B xylanophilus
GCF_007164525.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_B;s__Rubrobacter_B xylanophilus_A
GCF_004337705.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_C;s__Rubrobacter_C taiwanensis
GCF_003568865.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter;s__Rubrobacter indicoceani
GCF_000661895.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter;s__Rubrobacter radiotolerans
GCF_900175965.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter;s__Rubrobacter radiotolerans
GCA_013695475.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__;s__
GCA_013697315.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__;s__
GCA_013697825.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__;s__
GCA_013817025.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__;s__
GCA_014534485.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__;s__
GCA_016781635.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__;s__
VAL_E02-MAG-166  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__;s__
GCA_013695335.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SIRX01;s__
GCA_013696585.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SIRX01;s__
GCA_013812245.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SIRX01;s__
GCA_013812275.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SIRX01;s__
GCA_013813465.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SIRX01;s__
GCA_013815485.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SIRX01;s__
GCA_013815575.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SIRX01;s__
GCA_013820785.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SIRX01;s__
GCA_013821095.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SIRX01;s__
GCA_014534105.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SIRX01;s__
GCA_014534615.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SIRX01;s__
GCA_016781545.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SIRX01;s__
GCA_016781725.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SIRX01;s__
GCA_016781855.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SIRX01;s__
GCA_016781885.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SIRX01;s__
GCF_011492945.1  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SIRX01;s__
YEL_C01-MAG-155  d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SIRX01;s__
GCA_016781665.1  d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermobaculales;f__Thermobaculaceae;g__;s__
GCA_016781735.1  d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermobaculales;f__Thermobaculaceae;g__;s__
GCA_016781765.1  d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermobaculales;f__Thermobaculaceae;g__;s__
GCA_016781825.1  d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermobaculales;f__Thermobaculaceae;g__;s__
GCA_016781845.1  d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermobaculales;f__Thermobaculaceae;g__;s__
GCA_016781905.1  d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermobaculales;f__Thermobaculaceae;g__;s__
GCA_016781945.1  d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermobaculales;f__Thermobaculaceae;g__;s__
GCA_016781965.1  d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermobaculales;f__Thermobaculaceae;g__;s__
```

## Code
Mike's code doing the work is on this other page from one of my BRAILLE updates: 

https://hackmd.io/@astrobiomike/BRAILLE-notes-31-Mar-2021#Getting-Rubrobacter-genomes-in-NCBI