| as.treedata | as.treedata |
| as.treedata.phylo | as.treedata |
| beast-class | Class "beast" This class stores information of beast output |
| codeml-class | Class "codeml" This class stores information of output from codeml |
| codeml_mlc-class | Class "codeml_mlc" This class stores information of mlc file frm codeml output |
| drop.tip | drop.tip method |
| drop.tip,phylo | drop.tip method |
| drop.tip,treedata | drop.tip method |
| drop.tip-method | drop.tip method |
| get.fields | get.fields method |
| get.fields-method | get.fields method |
| get.fields-method | Class "jplace" This class stores information of jplace file. |
| get.placements | get.placements method |
| get.placements-method | get.placements method |
| get.placements-method | Class "jplace" This class stores information of jplace file. |
| get.subs | get.subs method |
| get.subs-method | get.subs method |
| get.tipseq | get.tipseq method |
| get.tipseq-method | get.tipseq method |
| get.tree | get.tree method |
| get.tree,beast | get.tree method |
| get.tree-method | Class "beast" This class stores information of beast output |
| get.tree-method | get.tree method |
| get.treeinfo-method | Class "jplace" This class stores information of jplace file. |
| get.treetext | get.treetext method |
| get.treetext-method | get.treetext method |
| get.treetext-method | Class "jplace" This class stores information of jplace file. |
| getNodeNum | getNodeNum |
| getRoot | getRoot |
| groupClade | groupClade method |
| groupClade-method | groupClade method |
| groupOTU | groupOTU method |
| groupOTU-method | groupOTU method |
| groupOTU.phylo | groupOTU.phylo |
| hyphy-class | Class "hyphy" This class stores information of HYPHY output |
| is.ggtree | is.ggtree |
| jplace-class | Class "jplace" This class stores information of jplace file. |
| label_branch_paml | label_branch_paml |
| mask | mask |
| merge_tree | merge_tree |
| Nnode | Nnode |
| Nnode2 | getNodeNum |
| Ntip | Ntip |
| paml_rst-class | Class "paml_rst" This class stores information of rst file from PAML output |
| phangorn-class | Class "phangorn" This class stores ancestral sequences inferred from 'phangorn' |
| phylip-class | Class "phylip" This class stores phylip tree(s) |
| phyPML | treeAnno.pml |
| pmlToSeq | pmlToSeq |
| print.beastList | |
| r8s-class | Class "r8s" This class stores output info from r8s |
| raxml2nwk | raxml2nwk |
| read.baseml | read.baseml |
| read.beast | read.beast |
| read.codeml | read.codeml |
| read.codeml_mlc | read.codeml_mlc |
| read.hyphy | read.hyphy |
| read.jplace | read.jplace |
| read.newick | read.newick |
| read.nhx | read.nhx |
| read.paml_rst | read.paml_rst |
| read.phylip | read.phylip |
| read.phyloT | read.phyloT |
| read.r8s | read.r8s |
| read.raxml | read.raxml |
| set.subs-method | Class "paml_rst" This class stores information of rst file from PAML output |
| set.subs<--method | Class "paml_rst" This class stores information of rst file from PAML output |
| show | show method |
| show-method | Class "jplace" This class stores information of jplace file. |
| show-method | show method |
| taxa_rename | taxa_rename |
| treedata-class | Class "treedata" This class stores phylogenetic tree with associated data |
| write.jplace | write.jplace |