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This seems like it would be useful, but not urgent.
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### Setup
I am reporting a problem with Biopython version, Python version, and operating
system as follows:
```
3.7.7 (default, Mar 23 2020, 02:22:49)
[Clang 11.0.0 (clang-1100.0.33.17)]
CP…
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Dear Charles,
Deepro and I are trying to create a stemmatic tree of MSS for his Saktumiva edition.
1. Output FASTA - okay (file 01output.fas)
2. mafft - apparently okay (file 02output-aligned.fas…
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Hi Cam,
the pmmd tags could be embedded into NeXML using semantic annotations. It makes some amount of sense to do this if PhyloMatic trees are merged into larger NeXML files that combine them, or ar…
rvosa updated
12 years ago
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Example based on issue reported on #334 by @yogeshhk (his was PhyloXML to Newick to NeXML):
```
$ python -c 'from Bio import Phylo; Phylo.convert("PhyloXML/phyloxml_examples.xml", "phyloxml", "oth…
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NeXML is an emerging standard, and the preferred way to import trees to OpenTree. We should try to support it eventually. NeXML is supported by the Python ETE library. Maybe we can add ETE to the Py…
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I am interested to develop an R package that would allow to interface with the open tree API (already mentioned in #14 by @dwinter, and in #3 by @arlin), so that the tree(s) and metadata can be manipu…
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If you (hypothetically) curate a study on devtree and then download it as nexml, and then upload it to the curation app it doesn't preserve the otu mapping or rooting etc.
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I've been looking into how to include content in NeXML that shows up as a `Group` value for a character, as in the Characters list panel in Mesquite. Looking that the NEXUS file saved by Mesquite, `Gr…
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I can't find instructions for how to build the Mesquite module for NeXML. Running maven as
```
$ mvn mesquite:build
```
yields the following error:
```
[INFO] ----------------------------…
hlapp updated
6 years ago