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All functions

as.treedata(<phylo>)
as.treedata
read.beast() read.mrbayes() read.beast.newick() read.mega()
read.beast
find.hclust()
find the hierarchical cluster analysis among the nodes of graph based on the length of all the shortest paths in the graph.
get.placements()
get.placements
get.tree()
get.tree
get.treetext()
get.treetext method
getNodeNum() Nnode2()
getNodeNum
is.ggtree()
is.ggtree
jplace-class
Class "jplace" This class stores phylogenetic placements
label_branch_paml()
label_branch_paml
mask()
mask
merge_tree()
merge_tree
print(<treedataList>)
print
raxml2nwk()
raxml2nwk
read.jtree()
read.jtree
read.astral()
read.astral
read.codeml()
read.codeml
read.codeml_mlc()
read.codeml_mlc
read.fasta()
read.fasta
read.hyphy()
read.hyphy
read.hyphy.seq()
read.hyphy.seq
read.iqtree()
read.iqtree
read.jplace()
read.jplace
read.mcmctree()
read.mcmctree
read.mega_tabular()
read.mega_tabular
read.newick()
read.newick
read.nextstrain.json()
read.nextstrain.json
read.nhx()
read.nhx
read.paml_rst()
read.paml_rst
read.phylip()
read.phylip
read.phylip.seq()
read.phylip.seq
read.phylip.tree()
read.phylip.tree
read.phyloxml()
read.phyloxml
read.r8s()
read.r8s
read.raxml()
read.raxml
read.treeqza()
read.treeqza
rename_taxa()
rename_taxa
rescale_tree()
rescale_tree
spt()
spt method
read.treetime() read.timetree()
read.timetree
write.jtree()
write.jtree
write.beast()
write.beast
write.beast.newick()
write.beast.newick
write.jplace()
write.jplace