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complicated commands that get generated by the parallel steps present a problem when working on systems using mpi. investigate whether we could instead write the commands to shell scripts and call tho…
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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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Hi,
My apologize if this if not the appropriate place to ask this.
I wondered if anyone had modified the code to compute the functional diversity according to the latest article of Chao et al. : h…
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**Short summary:** The runtime and memory consumption of `skbio.diversity.alpha._faith_pd` scale with the number of tips in the supplied phylogenetic tree and not with the number of features in the p…
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Hello, we get an installation failure with pip "ERROR: Could not build wheels for scikit-bio, which is required to install pyproject.toml-based projects" in a virtualenv using python 3.9，The specific …
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Title: A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology
# General Information
## Please paste a link to the paper or a citation here:
Link: https://www.biorxiv.…
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### Living_mulch_project
1. The overall goal. To test whether living mulch treatment lead to a more healthy soil microbiome community
Hypothesis to test
1. The soil microbiome community…
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Dear all, thanks for your fantastic work. How can we calculate the beta diversity of unweighted_unifrac, weighted_unifrac from your pipeline?
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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.