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The goal of this issue is to implement an efficient lineage tracking for `chainweb-data`. Currently, there's no efficient nor straightforward way to deduce lineage information about a block or any dat…
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From https://github.com/sars-cov-2-variants/lineage-proposals/issues/1662
S:T22N seems currently as fast as S:S31del globally. This derives by many different combinations so i think it is prudent …
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I am running the following command
```
checkm lineage_wf -f "mysample_downsample10pct_metabat.checkm.txt" -t 40 -x fa metabat_folder checkm_folder
```
Here is my traceback:
```
Traceback (…
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Currently all branches in the tree with equal depth have equal length. This should not be the case, as they should reflect cell division times. This will involve:
1. Calculating division times and cre…
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According to pangolin-designation v1.28, KR.2 has been redesignated as LT.1, however, pangolin-data v1.28 still assigns KR.2 instead of LT.1
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- [x] make taxon name much more prominent on page (hard to find now)
- [x] reverse order of breadcrumb / lineage: `life > child > child`
- [ ] different styles for Taxon, Synonyms, Lineage, Children
-…
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Dear Simon,
I am doing Discrete phylogeographic analysis for a dataset of 2600 influenza sequences following your paper. A Phylodynamic Workflow to Rapidly Gain Insights into the Dispersal History an…
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_Taken from **Branch 2** of sars-cov-2-variants/lineage-proposals#1962_
**Defining Mutations:** `MC.13` > `C23399G(S:Q613E)`
**Query:** `C10681T, A13121T, C23399G`
**Earliest seq:** 24-06-13 (`EP…
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Prior to delving into lineages at https://yulab-smu.top/treedata-book/chapter2.html#accesor-tidytree, it would be helpful to first simply explain how to do the basics, such as:
* Get all tip labels…
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```r
clonal.tree.generation(
bcr_clusters = clus$merged_fasta,
index = 200,
raw_data = raw$merged_fasta,
python_path = "/opt/miniconda/envs/repair/bin/python"
)
```
```
use defau…