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currently anvi'o pan and profile databases have a `clusterings` table that only supports newick formatted orders.
``` python
clusterings_table_name = 'clusterings'
clusterings_tabl…
meren updated
6 years ago
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The documentation has this command at the start of Part 3:
```
# format 16S copy number data
format_tree_and_trait_table.py -t ./genome_prediction/study_tree.tree -i gg_16S_counts.tab -o ./genome_p…
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Dendropy, while reading NEXUS consensus tree file created by MrBayes is converting dashes/hyphens "-" into " " or, when asked for preserving underscores, into underscores "_". This is not documented (…
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1. Currently when I run PASTML with no options it complains:
`Cannot find annotation file : PdP>`
It would be better to show the help message directly in this case.
1. If I run
`PASTML -h`
it …
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Input tree
```
"(((((((Homo sapiens,(Ara ararauna,Alligator mississippiensis)Archosauria)Amniota,Salamandra atra)Tetrapoda,Katsuwonus pelamis)Euteleostomi,Carcharodon carcharias)Gnathostomata,Asym…
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GreenGenes URL: http://greengenes.secondgenome.com/downloads/database/13_5
Tree file: gg_13_5_otus_99_annotated.tree.gz
Error message:
Traceback (most recent call last):
File "src/main/pytho…
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Add the following changes made during the proofs stage to the repository and preprint.
Page 2. Line 96. At the end of the sentence ending on this line add "that is sometimes directly incorporated int…
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Hi,
I have been using the designTree function in some of my scripts (thanks !) and became recently aware of a regression in this function, as it does not seem to return a correct design matrix anym…
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Hi David,
I'm using the newest version of OrthoFinder/2.2.0 (installed on HPC), however, I still got the error as the previous issue reported in Sep 2016. The error message was as below. Can you plea…
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Hi there,
I'm using the latest version of epa-ng and am getting this error when I try to run it:
```
terminate called after throwing an instance of 'std::runtime_error'
what(): Treeparsing …