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| as.treedata.phylo | as.treedata |
| drop.tip | drop.tip method |
| drop.tip,phylo | drop.tip method |
| drop.tip,treedata | drop.tip method |
| drop.tip-method | drop.tip method |
| get.placements | get.placements |
| get.placements.jplace | get.placements |
| get.tree | get.tree |
| get.treetext | get.treetext method |
| get.treetext-method | 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 |
| Nnode.treedata | Nnode |
| Nnode2 | getNodeNum |
| phyPML | treeAnno.pml |
| print.beastList | |
| raxml2nwk | raxml2nwk |
| read.astral | read.astral |
| read.beast | 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.mrbayes | read.beast |
| read.newick | read.newick |
| 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.phyloT | read.phyloT |
| read.r8s | read.r8s |
| read.raxml | read.raxml |
| rename_taxa | rename_taxa |
| taxa_rename | taxa_rename |
| write.beast | write.beast |
| write.jplace | write.jplace |
| write.jtree | write.jtree |