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In principle, we can build an XML that leads to the ancestral reconstruction of any MRCA of a set of taxa, or its parent if we want that. Specifications for taxon sets might also be useful for monophy…
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when i tried combine tree supports from two analyses onto one tree.
i got None/None
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currently no TC:
```
[Term]
id: GO:0043227
name: membrane-bounded organelle
namespace: cellular_component
def: "Organized structure of distinctive morphology and function, bounded by a single …
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Our phyloreferencing machinery uses [`excludes_lineage_to`](https://github.com/hlapp/phyloref/blob/c2a1b813690e3afc78c2abdacab216e368b5c83e/phyloref.owl#L61), which identifies a sibling to some ancest…
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With the addition of the PhyloTrees.jl and PhyloNetworks.jl packages to the julia ecosystem (#230), it is clear that the types ad methods provided by Phylo need yet another re-work.
Whilst the curren…
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Rather than only procedurally generated trees, we should reintroduce the ability to have defined trees. Either as a file reference or string in YAML config. Concern that the YAML string may prove prob…
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## Background
Issue https://github.com/OpenTreeOfLife/treemachine/issues/78 started because @ruchiherself's code identified cases in which a grouping in the synthetic tree conflicted with every tree …
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We need antheridium and archegonium in the PO. Consider adding gametangium as parent.
Proposed definitions:
Gametangium: A plant organ (or cardinal organ part?) that is part of a whole plant in the …