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Hi,
I would have a question regarding the use of tax_glom and rarefy_even_depth in phyloseq.
For my study, after having merged the tree, the metadata, the OTU table and taxonomy, I first used tax_…
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Briefly comment on this issue why you are interested in this mini-project.
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**Description**
**Sub-lineage of:** KP.3.1.1
**Earliest sequence:** 2024-9-8, Wales, EPI_ISL_19431531
**Most recent sequence:** 2024-10-2, Wales, EPI_ISL_19493965
**Continents circulating:** Europ…
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Hello -
I am working on analyzing alpha and beta diversity of a dataset.
I have imported data from DADA2, where I attempted to create a ML tree.
My problem is that I believe I have an ML tree wit…
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### Author(s) of proposal
Ran Wei
### Name of taxon
Lepisorus
### Rank of taxon
Genus
### Approximate number of species affected
_No response_
### Description of change
Lump…
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From @petrelharp:
> think the next thing to do is to figure out what we want to use it for - like, what things want to be computed? And, then, see if they can be computed easily this way. The que…
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Hi,
hope you're doing well.
I've been running phylophlan with the .log file stuck at this step for three days now: reducing number of RAxML threads to 20, as it appears to underperform with more thr…
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Hello!
I ran snippy-multi on a dataset of about 20 bacterial isolates (*.fasta assemblies) within the same genus (_Enterobacter_ spp.). The core genome length (from core.aln) was around 273,000 base …
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I've been trying to run:
`iNEXT.3D::AO3D(data=col_data,
diversity = div_type,
q = as.numeric(hill_number),
datatype = "abunda…
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I was trying to see the result of PD rarefaction using phyloRarefy as used by [Peralta et al (2015)](https://www.ncbi.nlm.nih.gov/pubmed/25279836), but realized that the function cannot rarefy the my …