-
Be nice to find the way to do this from our ITS data, leave clues to an approach here.
Ideally this would help us also assign unnamed OTUs to particular higher clades
-
_**EDIT**: Added `trees` element to the favorites JSON. Note that marking a favorite tree is distinct from marking a **study**._
The placeholder [`favorites-0` repo](https://github.com/OpenTreeOfLife…
-
The current method can cause issues on update, including:
- Excess files (minor)
- Incomplete unarchiving (intermediate)
- Incorrect index for clades (major)
-
Hi there
Maybe a basic question but I'd like to ask what people's opinion is of using DESeq2 within SQMtools for differential abundance of taxa? It's obviously possibly with SQMtools to compare dif…
-
### Context
In RSV I would like the root to belong to a clade so that any descendants that are not part of any other clade get that clade.
I'm not sure this is possible right now - it's relevant b…
-
Would it be possible to annotate nodes with taxonomy (higher-level names that are not reflected in the terminal names). Almost all phylogenies take a what we call 'exemplar approach' (Prendini 2001, h…
-
# Parsimony Diversity Exploration
We've been exploring the parsimony diversity of our simulated data, and trying to understand how various parameters of the simulation affect this summary statistic…
-
How can a user extract a subtree from OpenTree by specifying specific clades and pruning the giant tree down to the taxa desired? a la PhyloMatic or PhyloTastic
-
Hi! Thanks for the great package, I use parts of it routinely without issue.
I have a question about how to interpret the NAs sometimes outputted in boot.phylo() after using nj(dist(data_matrix)) …
-
Sorry, haven't done much homework on this, but is there a OT API mechanism to supply a topology only, and get back matching clades that exactly match that topology?