Output from EPA RAxML into reference tree

[vca007]

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Hi,

I have used RAxML EPA to place shorter reads of few OTUs onto a reference tree of longer sequences. My objective would be to obtain a tree incorporating the reference sequences with the Querry OTUs as new branches to their best location, and with the bootstrap values calculated from the reference tree building step. I have tried several approaches:

1. Using jplace and RAxML_bipartitionsBranchLabels outputs to merge them. However I can only vizualize branches of the reference tree and not the Querry OTUs.

2. Using the labelledTree from the Placement (containing reference sequences and Querries in the same tree) and the bootstraps values from RAxML_bipartitionsBranchLabels. However, if I try to merge them I get this:

tree_merged=merge_tree(labelledTree ,RAxML_bipartitionsBranchLabels) Error in merge_tree(labelledTree ,RAxML_bipartitionsBranchLabels) : input tree object is not supported...

Yet opening both trees separately are recognized by ggtree as phylogenetic tree.

And if I try to build ggtree from the tree separately, such as the command below, then I obtain a figure where the tree is on the left side and labels are hanging on the right. ggtree(labelledTree)+geom_tiplab()+geom_label(data=RAxML_bipartitionsBranchLabels,aes(label=bootstrap))

Would there be any method I am missing that could lead me to my objective? Thank you!