Base Classes and Functions for Phylogenetic Tree Input and
Output
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Documentation for package ‘treeio’ version 1.28.0
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| as.treedata.phylo | as.treedata |
| 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.placements.jplace | get.placements |
| get.tree | get.tree |
| get.treetext | get.treetext method |
| getNodeNum | 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 |
| Nnode2 | getNodeNum |
| print.treedataList | |
| raxml2nwk | raxml2nwk |
| read.astral | read.astral |
| read.beast | read.beast |
| read.beast.newick | read.beast |
| 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.jtree | read.jtree |
| read.mcmctree | read.mcmctree |
| read.mega | read.beast |
| read.mega_tabular | read.mega_tabular |
| read.mrbayes | read.beast |
| 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 |
| write.beast | write.beast |
| write.beast.newick | write.beast.newick |
| write.jplace | write.jplace |
| write.jtree | write.jtree |