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Hi,
the cfml_results.R script is throwing an error, and I'm having a difficult time figuring out how to resolve it. I've attached the CFML output files that I'm feeding into the script. I'm using R …
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We should look into an extended Newick format for singleton nodes, like [FigTree's](http://tree.bio.ed.ac.uk/software/figtree/) use of square-bracket enclosed, comma delimited strings for annotating n…
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hello,
I have picrust2-2.1.4-b, Python 3.6.7
Error running this command 1:
picrust2_pipeline.py -s sequences.fasta -i table.biom -o picrust2_out_pipeline -p 1
"FileNotFoundError: [Errno 2] No…
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Hi all,
I'm having some issues with the newick tree parser in Biopython. In particular, I think the parser doesn't work properly with the tree format that you obtain from PAML.
### Setup
I'm…
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I need a tree that is an exemplary or most expected BD tree in Newick format.
An exemplary BD tree has its branching times at the expected/idealized intervals.
The code below is definitely not a…
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This is the summary of our meeting today (@ozcan, @ShaiberAlon, @meren) during which we concluded that anvi'o needs a native 'gene view' mode, where every split is a gene with all perks of anvi-intera…
meren updated
5 years ago
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First of all thank you for the great package!
I encountered a problem when using the recent versions of ipyrad and toytree together:
python version: 2.7.15,
ipyrad version: 0.7.28 (py27ha9968…
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Hi,
It appears that the internal node labels from the reference tree are not present in the output file. Is there an option to preserve these labels?
Thanks.
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Hi,
Is there a way to keep the sample names in the rows of the output CNV plot?
For e.g. here the rows don't have any annotation so I can't figure out which row belongs to what sample.
[infe…