API for YuLab-SMU/treeio
Base Classes and Functions for Phylogenetic Tree Input and Output
| Global functions | |
|---|---|
| %<>% | Man page |
| %>% | Man page |
| .BStringSet2bin | Source code |
| .adjust.tree.network.edge | Source code |
| .as.phylo.rev.edges | Source code |
| .check.no.tree.network | Source code |
| .data | Man page |
| .internal.spt | Source code |
| .obtain.placement.char | Source code |
| .onAttach | Source code |
| .paste0_ | Source code |
| .paste1_ | Source code |
| .rev.edge | Source code |
| BEAST | Source code |
| MRCA | Man page |
| Nnode | Man page |
| Nnode2 | Man page |
| Ntip | Man page |
| add.branch.time.mcmctree | Source code |
| ancestor | Man page |
| as.phylo | Man page |
| as.phylo.dendro | Source code |
| as.phylo.ggtree | Source code |
| as.phylo.igraph | Source code |
| as.phylo.list | Source code |
| as.phylo.phylo4 | Source code |
| as.phylo.pvclust | Source code |
| as.phylo.tbl_df | Source code |
| as.phylo_hclust2 | Source code |
| as.phylo_hclust_node | 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 | Source code |
| as.treedata.pvclust | Source code |
| as.treedata.tbl_df | Source code |
| as_tibble | Man page |
| build_new_labels | Source code Source code |
| build_new_tree | Source code Source code |
| build_node_attrs | Source code |
| check.inode | Source code |
| check_attrs | Source code |
| check_edgelist | Source code Source code |
| check_num | Source code |
| check_value | Source code |
| child | Man page |
| drop.tip | Man page |
| edge2vec | Source code |
| edgeNum2nodeNum | Source code |
| extract.placement | Source code |
| extract_another | Source code |
| extract_attrs | Source code |
| extract_node_attrs | Source code |
| extract_treename | Source code |
| extract_values_attrs | Source code |
| filename | Source code |
| fill_id | Source code |
| find.hclust | Man page Source code |
| find.hclust.igraph | Source code |
| full_join | Man page |
| 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 |
| getNodeName | Source code |
| getNodeNum | Man page Source code |
| getPhyInfo | Source code Source code |
| getSubsLabel | Source code |
| get_seqtype | Source code |
| getnewplacements | Source code |
| getplacedf | Source code |
| guess_fasta_type | Source code |
| has.slot | Source code |
| inner_join | Man page |
| is.ggtree | Man page Source code |
| is.rooted | Man page |
| is.tree | Source code |
| isTip | 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 |
| nodelab | Man page |
| offspring | Man page |
| old_new_node_mapping | Source code |
| parent | Man page |
| parser_children | Source code |
| parser_clade | Source code |
| paste_nested_list | 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.beast.newick | 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.mcmctree | 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.nextstrain.json | Man page Source code |
| read.nexus | Man page |
| read.nhx | Man page Source code |
| read.nhx.stats | Source code |
| read.nhx.tree | 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.timetree | Man page Source code |
| read.tip_seq_mlc | Source code |
| read.trans_beast | Source code |
| read.tree | Man page |
| read.treeqza | Man page Source code |
| read.treetext_beast | Source code |
| read.treetime | Man page Source code |
| reexports | Man page |
| remove_names | Source code |
| remove_quote_in_tree_label | Source code |
| rename_taxa | Man page Source code |
| rescale_tree | Man page Source code |
| root | Man page |
| rootnode | Man page |
| rtree | Man page |
| set_branch_length | Source code |
| set_substitution | Source code |
| single_tree | Source code |
| spt | Man page Source code |
| spt.igraph | Source code |
| string2DNAbin | Source code |
| summarize_placement | Source code |
| tibble | Man page |
| tipIds | Source code |
| treedata | Man page |
| treeio | Man page |
| treeio-package | Man page |
| write.beast | Man page Source code |
| write.beast.newick | Man page Source code |
| write.jplace | Man page Source code |
| write.jtree | Man page Source code |
| write.nexus | Man page |
| write.tree | Man page |
