Feature: infer species tree from gene tree

fmarotta / recPhylo

Parse recPhyloXML and phyloXML files in R.

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Feature: infer species tree from gene tree #1

Closed fmarotta closed 2 months ago

fmarotta commented 6 months ago

We should add a way to automatically infer a species tree from a gene tree. This paves the way to:

full support of the recPhyloXML specification
support for bifurcationOut events and free living species

fmarotta commented 3 months ago

...on second thought, how can we infer the species tree when the gene tree has branchingOut events? Also, what if there are multiple phylogenies in the recGeneTree? Besides, bifurcationOut does not require drawing a species tree, we just need to add a plotting area outside of the species tree and dump the bifurcating clades there.