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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…
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The benchmark currently reports "accuracy" at each taxonomic level. It would ideally report precision and recall of placement, along with the F1 score. These metrics could be reported on a per-organis…
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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…
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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…
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Use a well characterized dataset to understand whether the automatically generated SSU-Align alignments are sufficient for phylogeny.
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`guppy pentropy` should be renamed `guppy entropy`, with two entropy measures:
- phylogenetic entropy (see #189)
- quadratic entropy, described in a phylogenetic context in this [paper](http://dx.doi…