JuliaPhylo / PhyloNetworks.jl

A Julia package for statistical inference, data manipulation and visualization of phylogenetic networks
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plot alternative bootstrap hybridizations on best network #66

Open crsl4 opened 6 years ago

crsl4 commented 6 years ago

I created a function that will add other hybridizations found in bootstrap networks to the best estimated networks with snaq. By default, the function adds the three best alternative hybridizations (that match with the underlying tree topology), as long as the bootstrap support is greater than 10%. The function is not exported yet because I still need to make more tests. The procedure is:

bootnet = readMultiTopology("bootstrap-networks.txt")
bestnet = readTopology("best.tre")
BSn, BSe, BSc, BSgam, BSedgenum = hybridBootstrapSupport(bootnet, bestnet);
PhyloNetworks.addAlternativeHybridizations!(bestnet,BSe)
plot(bestnet, edgeLabel=BSe[[:edge,:BS_hybrid_edge]])

The new hybridizations are hard to distinguish from the original hybridizations in the best network. The only difference is that the new added hybridizations only have bootstrap support for the minor hybrid edge. However, it would be nice if these new hybridizations are plotted in a different color (or dashed line). I write this here in case someone has time to look into this. Otherwise, I sill have it in my to-do list and will try to get back to it soon.

gaballench commented 9 months ago

@crsl4, is this what we did recently for the fish and plant datasets?