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We should consider adding a rule or two to automatically compute alpha diversity and maybe do some simple beta-diversity plots on all input samples, as that is often requested by people.
I'm think…
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Hi,
I am using _**list**_ command to get the sub-trees for 3 taxa of _[11050, 11103, 11108]_, the result is different for different orders of these taxa. i.e.:
When I call **taxonkit list --ids ..…
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Hi! Trying to use the latest builds fails to download data with the following errors:
mamba create -y -n gtotree -c astrobiomik
e -c conda-forge -c bioconda -c defaults gtotree
…
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### Prerequisites
taxonkit v0.9.0
go version go1.17.7 linux/amd64
### Describe your issue
wget -c https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz
sed '1d' prot…
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https://mp.weixin.qq.com/s/xqO7Wur2cMLLwRUSgR1yuQ
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@vinisalazar wrote:
> I was also able to run some fastsubtrees-query commands, which got me thinking it would be nice to have other attributes of a taxonomy entry (e.g. Scientific Name, Lineage, etc)…
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Dear developers,
I have read that in your `collect module`, genomes from various sources will be downloaded. Is it possible to specifiy a list of species to download? For example, a list contains s…
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Thanks for creating these taxonomy files. I was trying to use the files from R207 to build a Diamond database, however it failed when reading the `names.dmp` with the following error message: `Failed …
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I didn't do any systematic evaluation, but I found at least one lineage that skips the family level:
```python
taxon = taxopy.Taxon(619996715, taxdb)
print(taxon)
# s__Bacteria;p__Patescibacteri…
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@vinisalazar wrote
>I was also able to run some fastsubtrees-query commands, which got me thinking it would be nice to have other attributes of a taxonomy entry (e.g. Scientific Name, Lineage, etc) i…