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 |