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Ross Mounce:
almost all newick files have one or more missing tip labels so today I'm just going to plough through adding in the missing labels, manually. After this is done I will do GenBank lookup …
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Example from the API docs is not working,
(https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-of-Life-APIs#find_trees)
```
curl -X POST http://api.opentreeoflife.org/v2/studies/find_trees -H …
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More specifically, for a `nexml` object `nex`, the lists resulting from
```R
sapply(nex@characters[[1]]@format@char, slot, "label")
```
and
```R
colnames(get_characters(nex))
```
will be set e…
hlapp updated
5 years ago
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Following up on discussion at https://groups.google.com/forum/#!topic/opentreeoflife/Cj1tw2jWnAc : if someone uses an external tool to do TNRS on names, allow them to upload a tree via the web curatio…
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Many trees have an ingroup/outgroup distinction, which affects both data collection and biological conclusions. Knowing the ingroup, when one is known, is essential for meaningful scientific use of tr…
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something like `Tree.from_biopython(...)` and `Tree.as_biopython(...)`
1) The method should accept/return biopython Tree instances.
2) Is it possible to avoid newick serialisation?
3) any special at…
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Due to a [minor UI bug](https://github.com/OpenTreeOfLife/opentree/issues/985) (now fixed), this property was not being set in the web-app UI, and in many cases it will be empty. We might want to swee…
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This should be 3 issues; I think there may be issues for some/all of these. Sorry I did not want this to fall through the cracks, and I was afraid that I'd forget...
1. I think that meta tags of type …
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Ross Mounce wrote:
```
##Pre-processing steps
#Put all Newick trees into one file, one per line
for i in *.nwk ; do cat $i >> testree.tre ; sed -i -e '$a\' testree.tre ; done
#Remove Newick strings …