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Because of the way in which phyloreferences are constructed, we know that they sometimes resolve to more than one node. One example we have of this is a phyloreference adapted from [Brochu 2003](https…
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貼吧活動:(請查閱 [SARS-CoV-2 Timeline by 2020.02.21](https://github.com/agorahub/_meta/blob/agoran/theagora/sari/Memorandum_2020-02-21_SARS-CoV-2-Timeline_Nathan.pdf?raw=true), by Nathan :cloud: )
- Colla…
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In PR #230, I removed the following example files:
* fisher_et_al_2007.json (from https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2)
- Includes an apomorphy-based definitio…
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1) I think we should all together discuss if these are the definitions and terms that we want to use:
"the term pangenome is defined as the entire set of genes from all strains of a clade."
The comp…
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*************edited November 20***************
**TRACKER**
BA.2.86: -C6541T,A7842, C8293T, G8393A (new query thx to @aviczhl2 )
JN.1 QUERY: C18894T, T15756A, A7842, -C6541T
XDD Query : C6541T…
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When I want to identify a clade of interest, I want to be able to filter clades based on a case definition (i.e., epi metadata) so that I can see which clades are most relevant to my investigation. …
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Here is a file to edit: https://drive.google.com/file/d/1YG5dy3rDf3BSuy7p6MhP7weNw5o-jTE8/view?usp=sharing
**It contains:**
- the list of existing concepts
- a list of the values already mapped…
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I have been trying to use augur to draw a phylogenetic tree.
the command I am using is as follows:
augur clades --tree Omicron_refined_tree.nwk --mutations Omicron_aa_muts.json ncov_nt_muts.jso…
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Currently clades are defined independently of one another in the provided TSV, but we often duplicate the mutations of a parent clade. For example, 21L is a descendant of 21M so we have the following:…
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**Context of the feature request related to a problem:**
We would like to better model MONDO biological inheritance (see https://github.com/monarch-initiative/monarch-ingest/issues/295)
**Workin…