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I have just noticed that the binomial lookup correction isn't making it into the output Newick files.
There are lots of pairs of taxa, where one is obviously a mispelling variant in my MRP matrix fil…
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To create a tool which removes tip nodes (primarily because they have no labels). This should be done on `nexml` . Any resultant poorly formed nodes (e.g. with 1 or 0 children) should be deleted/tidie…
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In this study, I wanted to export as nexml but get "Exception in coercing to the required NexSON version for validation. "
https://devtree.opentreeoflife.org/curator/study/edit/tt_200?tab=metadata
No…
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One of the projects I thought was really interesting back in Phylotastic II was PhyloStyloTastic (PST: http://www.evoio.org/wiki/PhyloStyloTastic). The idea behind PST is simple:
1. NeXML file contain…
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The `symbol` attribute for `AbstractState`, which `StandardPolymorphicStateSet` inherits from, is defined as `xs:anySimpleType`, so presumably anything should go, including "1 and 0".
That's in con…
hlapp updated
5 years ago
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Our group needs to extend NeXML to include references to images: https://github.com/SpeciesFileGroup/taxonworks/issues/2142
* We would prefer to do it in a block at the end of the file, rather than…
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Taxon names can be ambiguous due to synonymies and homonymies. To facilitate integration of returned trait data matrices with other trait data, having also identifiers for taxa rather than just names …
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`phylo2owl.py` currently writes out all the nodes found in the input tree file so it _should_ work with phylogenetic networks that aren't trees if DendroPy can parse them. If this is a necessary featu…
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After the search finishes, the user needs to be able to save trees to an output file (which the user can name). The output is a .tre file, which is basically just a different kind of nexus file.
Exam…
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It's not clear to me what name was settled on. Is it nexss, tss, or treess? I just want to make sure we're consistent.
nexss sounds like "nexus" and seems to tie the concept to closely to nexml. tree…