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