-
List lookups are the devil. This is an awkward one to work through. Essentially, parallel beta diversity gets a [phylogenetic row metric](https://github.com/qiime/qiime/blob/master/qiime/beta_diversit…
-
Hi,
I was willing to use Phyloseq to visualize some metagenomics results from our project MG7 ( https://github.com/pablopareja/MG7 ).
I've been having a look at the Biom format http://biom-format.org…
-
> It would be helpful to have phylogenetic trees for the four clades as supporting figures, since as best I understand Figure 2 and 3 do not represent the phylogenetic relationships, but only show the…
trvrb updated
11 years ago
-
Thanks for a great package, I'm impressed with many of the functions in phyloseq! I've used it to import my qiime data into R and to plot many diversity plots. One of the motivations for trying phylos…
-
When using alpha_rarefaction.py with the observed_species metric (which is non-phylogenetic), the workflow failed at the alpha_diversity.py step because the alpha_diversity.py commands contain '-t Non…
-
Phylogenetic placement of reads that are very close to a reference sequence would be more accurately placed using their DNA sequence. We should identify these reads/sequences on the basis of rapsearch…
-
PhyloSift will use a program from the user's path rather than the built-in version in metAMOS/phylosift. This can cause errors if an incorrect version is installed. Example failure:
PhyloSift -- Phyl…
-
Merge `wpd`, `pd`, and `entropy` into a single subcommand: `guppy fpd`
`guppy fpd` should be similar to `guppy entropy`, with a few modifications:
- add a `pd` column with phylogenetic diversity
- ad…
-
Hi,
I had successfully started the pipeline with the following command:
DATA="/home/dbrami/tmp/metAmos"
/tmp/PhyloSift/phylosift_20120412/bin/phylosift all --output=results --threaded=20 --debug --pa…