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Hello - does anyone know how a phylogenetic tree is updated when a phyloseq object is filtered and/or pruned? Doesn't a phylogeny change every time you add or remove taxa? How does phyloseq take into …
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I'd like to perform diversity analysis based on unifrac distance. however, I have no idea how to get phylogenetic tree conveniently. The taxonomy names and IDs obtained from kraken2 failed to be recog…
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A. Alpha diversity
a) Metrics – richness, phylogenetic diversity, Shannon Index)
1) Coefficient of variation (CV = standard deviation/mean) – useful to compare the variation of two populations indepen…
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**Addition Description**
Allow developers to add a `sort_name` to their methods. Sort methods by `sort-name` first, defaulting to `name` if no `sort_name`.
**Current Behavior**
Methods are sorte…
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AFAIK, the documentation requested by the author of [this post](https://groups.google.com/forum/#!topic/qiime-forum/K2Bufi7qhas) on the QIIME forum does not exist.
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## Tissue (DNA) database of BHHU-ATRA
Dataset link: https://www.bhhuatra.com/en/tissue-dna-database
Region: Bosnia and Herzegovina
Taxon: amphibians and reptiles
Type: undefined
Why is this impor…
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### Ancestral Sequence reconstruction
Benefits for Beast
https://groups.google.com/g/beast-users/c/P4_buh3u_5A
### a pilot test with Smith.et.,al data
1. EPICC score was calculated only wi…
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I've uploaded the file 'CommunityMat' that works as a community matrix for the animals. Together with the nwk file from TimeTree, I'm able to calculate the phylogenetic diversity for the animals with …
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While we have in theory, a record of some layer usage via logs, it is probably not comprehensive. Ideally, we need to capture all usage of a layer (display only or in Tools). Ideally, I would like to …
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Deep paging is limited to a 100,000 offset, but breaks at 10,000
E.g. using [9980 works](https://api.gbif.org/v1/species/search?rank=SPECIES&highertaxon_key=359&status=ACCEPTED&datasetKey=d7dddbf4-…