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Homology search started at 2024-08-21 08:40:06.163220.
Settings:
Search method: diamond.
Self-alignment method: native.
Remote fetch enabled: no.
Reading input proteins...
Sulfurospirill…
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The strategic partnerships tax_ids updated in tool spreadsheet:
https://docs.google.com/spreadsheets/d/1gsajrt_V-6rZxAoqD62O6H_y0ZDVVSwkPKGT99bBqHM/edit?gid=1917662552#gid=1917662552
https://gi…
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Hi,
this is a feature request.
In the documentation there is the following example:
```
from ete3 import NCBITaxa
ncbi = NCBITaxa()
tree = ncbi.get_topology([9606, 9598, 10090, 7707, 8782])
p…
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Hi,
I hope to gain taxonomy info while running taxonkit and csvtk using`-t`, which is helpful for me to import the result into R. But R and excel seems to have trouble importing the result. Some l…
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**Describe the bug**
I am encountering an error when downloading genome summary for the 2975324 taxid
**Version**
```sh
$ datasets version
datasets version: 16.27.1
```
**To Reproduce**
`…
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if 10239 in ncbi.get_lineage(int(sp)):
File "/home/jingtian/software/miniconda3/envs/py3/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 241, in get_lineage
raise ValueE…
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It would be useful to have the NCBI taxid of the last non-"dropped" taxon added to the collapsed taxonomy table. There was some attempt to do this already, but it turns out to be tricky. We can't just…
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Support string names or int taxids
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Hi,
I am using taxonkit lineage, and it works wonderfully so far. But there are a few species it seems not to be finding, despite their presence on the NCBI taxonomy portal.
I am not sure how th…
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**Current term details**
Currently the term host_taxid is specifically for the NCBI taxonomy, should we expand this to allow use of other species taxonomies?
```
Term name - host taxid
Term ID -…