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Tree: https://github.com/naturalis/RiseAndFall/blob/master/tree_inference/results/mammals/mammals_phylogeny/mammals_phylogeny_corrected_iucn.nex
Internal phylogeny of cervidea does not make any sen…
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Tree: https://github.com/naturalis/RiseAndFall/blob/master/tree_inference/results/mammals/mammals_phylogeny/mammals_phylogeny_corrected_iucn.nex
The phylogeny of muridae is completely off. Gerbilli…
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Need a scheme to translate names to emojjy, but with a suitable phylogeny framework in Python should be straight forward from there onwards
e.g. using ete3
```
from ete3 import Tree
import py…
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This is such a mess that it's hard to know where to begin. Genomic analyses and morphological studies place gastropods and bivalves as sister taxa. Within Bivalvia, the first branch is Protobranchia…
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**Which GENERA tool**
Give here the name of the tool:
Phylogeny
**More about**
Explain below what is unclear:
I got the following error:
```
`executor > local (5)
[bd/3341da] process …
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In `create-genome-phylogeny` no list for "all". RAXML also errors with options
```
# different ribosomal markers for archaea/bacteria/all
bacteria_list = ['rpL14_bact','rpL15_bact','rpL16_bact',…
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Hello,
I want to have an OTU table in which OTUs are identified by feature id and/or consensus sequence instead of by an assigned taxonomy (so that I can do phylogenetic analysis that isn't database …
irc47 updated
2 weeks ago
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Sorry to bother you both @dan-knight @whelena !
I was trying to plot one emulsiphy result and got this error. I was wondering if this is an edge case with multiple root nodes, or it is something co…
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Hi,
I'm trying to run on the example dataset using the command
`python ~/Broccoli/broccoli.py -dir ~/Broccoli/example_dataset/ -ext '.fasta'`
with diamond version 4.0.515 and fasttree versio…