Hybrid detection with MSCQuartets

To compare the hybrid detection results from HyDe, we will run MSCQuartets in R.

In results:

library(MSCquartets)

gtrees=read.tree(file="09-all_gene_trees_snaq.tre")
tnames <- unique(unlist(lapply(gtrees, function(x) x$tip.label)))

QT=quartetTable(gtrees,tnames)
RQT=quartetTableResolved(QT)

pTable3=quartetTreeTestInd(RQT,"T3")
quartetTablePrint(pTable3[1:6,])

write.csv(pTable3, "12-mscquartets-ptable.csv")