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Hi
Firstly, thanks for developing such a great tool! I've had an odd issue occur whereby some zero-length branches in the reference tree get replaced with a branch length of 0.1053605157 in the epa…
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Hi @idaios
I prepare my dataset from scratch having high quality 10 sars-cov2 genome with 2 outgruop so total sequences in my data are 12 for which I again ran all script, this time I am stuck at …
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Detailed future work ideas, such that we can remove them from the supplement:
\section{Detailed Future Work Ideas}
\subsection{Runtime Improvements}
\subsubsection{Improve virtual re-rooting du…
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The annotation DB will contain many different targets, and it would be interesting to be able to easily see / query those definitions. This could also potentially lead to re-use of definitions for the…
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Hello!
I am processing ITS data with DADA2 (primers ITS1F-ITS2). I am following recommendations from this paper (https://www.sciencedirect.com/science/article/pii/S1754504818302800?via%3Dihub) and fo…
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Hello,
I tried to redo a tree of life including my own metagenomes (~488) using the approach that you provide in examples (log file:
[phylophlan_tol.log](https://github.com/biobakery/phylophlan/fi…
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It would be nice to have empress automatically label internal with a taxonomy if a user provided a taxonomy .qza file. I thought we had this feature already implemented but after a discussion with Imr…
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Hello,
I'm looking to create a custom database to run in Phylosift and keep getting error messages when trying to build the database using The Monkey. I can index the created database, but the taxa …
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Hi,
The following job fails:
java -cp scripts/java/PEWO_java/dist/PEWO.jar DistanceGenerator_LITE2 /home/balaban/PEWO/examples/1_fast_test_of_accuracy_procedure/run RAPPAS,EPANG,PPLACER &> /home…
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These are from SILVA, but seem to have no subtaxa, and may simply be RNA sequence clusters. Not sure if anything need to be done about this or not, to if it is symptomatic of a general SILVA issue
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