API for treeio
Base Classes and Functions for Phylogenetic Tree Input and Output
| Global functions | |
|---|---|
| %>% | Man page |
| .BStringSet2bin | Source code |
| .onAttach | Source code |
| BEAST | Source code |
| MRCA | Man page |
| MRCA.phylo | Source code |
| MRCA.treedata | Source code |
| Nnode | Man page |
| Nnode.treedata | Man page Source code |
| Nnode2 | Man page |
| Ntip | Man page |
| Ntip.treedata | Source code |
| ancestor | Man page |
| ancestor.phylo | Source code |
| ancestor.treedata | Source code |
| as.phylo | Man page |
| as.phylo.ggtree | Source code |
| as.phylo.hclust_node | Source code |
| as.phylo.igraph | Source code |
| as.phylo.phylo4 | Source code |
| as.phylo.pvclust | Source code |
| as.phylo.tbl_df | Source code |
| as.treedata | Man page |
| as.treedata.ggtree | Source code |
| as.treedata.phylo | Man page Source code |
| as.treedata.phylo4 | Source code |
| as.treedata.phylo4d | Source code |
| as.treedata.pml | Man page Source code |
| as.treedata.pvclust | Source code |
| as.treedata.tbl_df | Source code |
| as_tibble | Man page |
| as_tibble.pvclust | Source code |
| check_attrs | Source code |
| check_edgelist | Source code |
| check_value | Source code |
| child | Man page |
| child.phylo | Source code |
| child.treedata | Source code |
| drop.tip | Man page |
| drop.tip,phylo | Man page |
| drop.tip,phylo-method | Man page |
| drop.tip,treedata | Man page |
| drop.tip,treedata-method | Man page |
| drop.tip.treedata | Source code |
| edgeNum2nodeNum | Source code |
| extract.placement | Source code |
| extract_another | Source code |
| extract_values_attrs | Source code |
| filename | Source code |
| fill_id | Source code |
| full_join | Man page |
| full_join.phylo | Source code |
| full_join.treedata | Source code |
| get.data | Man page |
| get.fields | Man page |
| get.placements | Man page Source code |
| get.placements.jplace | Man page Source code |
| get.subs_ | Source code |
| get.tree | Man page Source code |
| get.treetext | Man page |
| get.treetext,treedata-method | Man page |
| getNodeName | Source code |
| getNodeNum | Man page Source code |
| getPhyInfo | Source code |
| getSubsLabel | Source code |
| get_seqtype | Source code |
| getnewplacements | Source code |
| getplacedf | Source code |
| gfocus | Source code |
| groupClade.phylo | Source code |
| groupClade.treedata | Source code |
| groupOTU.phylo | Source code |
| groupOTU.treedata | Source code |
| guess_fasta_type | Source code |
| has.slot | Source code |
| is.ggtree | Man page Source code |
| is.rooted | Man page |
| is.rooted.treedata | Source code |
| is.tree | Source code |
| isTip | Man page Source code |
| isTip.phylo | Man page Source code |
| isTip.tbl_tree | Man page Source code |
| isTip.treedata | Man page |
| is_numeric | Source code |
| jplace-class | Man page |
| jplace_treetext_to_phylo | Source code |
| label_branch_paml | Man page Source code |
| mask | Man page Source code |
| matrix2vector.phyDat | Source code |
| matrix2vector.phyDat.item | Source code |
| merge_tree | Man page Source code |
| mergenm | Source code |
| nodeIds | Source code |
| nodeid | Man page |
| nodeid.phylo | Source code |
| nodeid.treedata | Source code |
| nodelab | Man page |
| nodelab.phylo | Source code |
| nodelab.treedata | Source code |
| offspring | Man page |
| offspring.phylo | Source code |
| offspring.treedata | Source code |
| parent | Man page |
| parent.phylo | Source code |
| parent.treedata | Source code |
| parser_clade | Source code |
| pmlToSeqString | Source code |
| print.treedataList | Man page Source code |
| raxml2nwk | Man page Source code |
| read.astral | Man page Source code |
| read.beast | Man page Source code |
| read.codeml | Man page Source code |
| read.codeml_mlc | Man page Source code |
| read.dnds_mlc | Source code |
| read.fasta | Man page Source code |
| read.hyphy | Man page Source code |
| read.hyphy.seq | Man page Source code |
| read.iqtree | Man page Source code |
| read.jplace | Man page Source code |
| read.jtree | Man page Source code |
| read.mega | Man page |
| read.mega_tabular | Man page Source code |
| read.mrbayes | Man page |
| read.newick | Man page Source code |
| read.nexus | Man page |
| read.nhx | Man page Source code |
| read.paml_rst | Man page Source code |
| read.phylip | Man page Source code |
| read.phylip.seq | Man page Source code |
| read.phylip.tree | Man page Source code |
| read.phyloxml | Man page Source code |
| read.r8s | Man page Source code |
| read.raxml | Man page Source code |
| read.tip_seq_mlc | Source code |
| read.trans_beast | Source code |
| read.tree | Man page |
| read.treetext_beast | Source code |
| reexports | Man page |
| remove_quote_in_tree_label | Source code |
| rename_taxa | Man page Source code |
| reroot_node_mapping | Source code |
| rescale_tree | Man page Source code |
| root | Man page |
| root.phylo | Man page Source code |
| root.treedata | Man page Source code |
| rootnode | Man page |
| rootnode.phylo | Source code |
| rootnode.treedata | Source code |
| rtree | Man page |
| set_branch_length | Source code |
| set_substitution | Source code |
| sibling.phylo | Source code |
| single_tree | Source code |
| string2DNAbin | Source code |
| summarize_placement | Source code |
| tipIds | Source code |
| tree_subset | Man page Source code |
| tree_subset.phylo | Man page Source code |
| tree_subset.treedata | Man page Source code |
| tree_subset_internal | Source code |
| treedata | Man page |
| write.beast | Man page Source code |
| write.jtree | Man page Source code |
| write.nexus | Man page |
| write.tree | Man page |
| write_beast_newick | Source code |
