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Dear @jsilve24
My dataset contains a combination of bacterial hierarchical information and phylogenetic relationship between samples.
I went through both "pibble" and "basset" vignettes, I was …
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**Describe the bug**
Nodes and links are not colored when the 'Leaves' and 'Branches' color settings are selected. However, node and link colors display correctly in the 2D network.
**To Reproduce…
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Suggestions provided by @haruosuz
- bactopia can accept GFF3 files (.gff) instead of FASTA files (.fna) as input, like PIRATE and Roary, to skip Prokka?
- bactopia can do alignment trimming (e.g. …
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Ross Mounce:
I have discovered that some programs don't like "singleton nodes" p4 may also be having this problem
so trees like this:
```
((X76436:483.0,((X60646:436.0,(ABOZ1185:296.0,(D16268:208.0,(…
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Good afternoon,
I am having trouble running MP-EST v 3.0 both on my institution's linux cluster and on the research group's mac. Both times I am able to run the test dataset without any issues. It…
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Hi @jeetsukumaran,
Before I continue reporting on this error, just want to say a big thanks for putting out this library. It's come in really useful for a few papers we've written.
For a project t…
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I was wondering if it was worth looking at within signature differences to get an idea of the diversity of hashes? i.e using Jaccard, Hammings or Lenvestein metrics.
I need to check my understanding…
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I've got a phylogeny that I'd like to annotate but am having issues. The annotation data is in the form of
This code works:
```
p
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Choose one of the following additional visualizations:
- A visualization designed by your team showing the unstructured text data about habitat and substrate. This data is not available for all sam…
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One of the projects I thought was really interesting back in Phylotastic II was PhyloStyloTastic (PST: http://www.evoio.org/wiki/PhyloStyloTastic). The idea behind PST is simple:
1. NeXML file contain…