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Hello !!
Is there any way to generate a phylogenetic tree from Bracken output. I aim to estimate phylogenetic diversity (exp: Faith PD)?
Regards
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These issues came up in the context of #1027. These are also related to #1040.
- [ ] port original UniFrac web docs
~~- [ ] explore alternative weighting schemes (see @rob-knight's comment [here](h…
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### Context
The glycoprotein complex (GPC) is the only surface protein of the Lassa virus (LASV) and plays a crucial role in mediating entry into host cells. It is also a primary target for neutr…
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A PSV/PSE/PSC/etc version that can handle really big phylogenies. In the past I have tried to calculate PSV on a phylogeny with several hundred thousand tips, but R will give a 'cannot allocate vector…
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**Is your feature request related to a problem? Please describe.**
It would be great if phylogenetic beta diversity was accessible via a script so it could be called from the command line.
**Descr…
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Hi @nickallsing @nallsing-salk
Very interesting research you guys did. I was trying to replicate your methodology but then I figured there were no qiime analysis scripts. I managed to import the mod…
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**Bug Description**
When working with a Python method the docstring indicates that the return type is some subclass of the `Artifact` class, however the return type seems to always be of type `Result…
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number of families
phylogenetic diversity
number of genera
evenness
within- and between-plot beta-diversity
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Hello
I have the following exception when using the following line:
> WU=skbio.diversity.beta_diversity("weighted_unifrac", gen3.values, ids=ids2, tree=st_imp, otu_ids=taxids_n_str)
> Traceback (…
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In week 3 the general focus is on phylogenetic and functional diversity. If we make week 2's assignment about the niches of domesticated animals (ungulates), then week 3 should be about the functional…
rvosa updated
5 years ago