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```[tasklist]
### `KP.3.3.1` Recombinant Islands
- [ ] [Branch 1](#branch_1) : `KP.3.3.1` and `KS.1` recombinant gaining `S:F59S` and `S:R346T` [query: `C6568T, T21738C, C23039G`, 5 seqs, Canada…
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If a phylogenetic tree was generated using likelihood searches under data partitioning. How to get the model parameters?
I have a reference tree that was generated by 10 partitions. My query sequen…
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# Intro
- Problem statement:
* NCBI records vary in quality
* not available for download as a single data set
* annotation not consistent or difficult to piece together
- Previous 16S data…
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This is a feature request. Currently dnConstrainedTopology only accepts TimeTree distributions for the treeDistribution argument (and I've only succeeded in using it with dnBDP in particular). This wo…
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Hi, I'm trying to convert the jplace table but it seems like my jplace file has no entries for `multiclass`. Can you explain why this is? I was assuming that the jplace files are the same as the outpu…
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Hello,
I was using GTDBtk to classify several genomes and found a file with RED values for pairs of genomes in the dabatase used, which I assumed was calculated from the Bac120 tree (and confirmed us…
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I calculated the crossmapping between the transcriptomes to assess and have an idea of how common it is and its distribution.
We have closely related transcriptomes (RCC1587 and RCC1693), somewhat…
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Hi,
The table.biom file seems to be just a feature table, so how do I get a similar feature otu sequence, like a 16s analysis. I'm also confused by the tree.qza used in the ogu.md for "OGU analysis…
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I've been playing around with GARD and ran it on 10 and 20 randomly sampled Pango sequence founders.
When I tried it out on 27 sequences, however, I got an error:
```
hyphy gard --alignment sa…
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Hi Lucas,
I just read your paper on _**Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples**_, which illustrated the benefits of incorporating phylogeny int…