Man pages for Bioconductor-mirror/treeio
Base Classes and Functions for Phylogenetic Tree Input and Output

as.treedataas.treedata
beast-classClass "beast" This class stores information of beast output
codeml-classClass "codeml" This class stores information of output from...
codeml_mlc-classClass "codeml_mlc" This class stores information of mlc file...
drop.tip-methodsdrop.tip method
get.fields-methodsget.fields method
getNodeNumgetNodeNum
get.placements-methodsget.placements method
getRootgetRoot
get.subs-methodsget.subs method
get.tipseq-methodsget.tipseq method
get.tree-methodsget.tree method
get.treetext-methodsget.treetext method
groupClade-methodsgroupClade method
groupOTU-methodsgroupOTU method
groupOTU.phylogroupOTU.phylo
hyphy-classClass "hyphy" This class stores information of HYPHY output
is.ggtreeis.ggtree
jplace-classClass "jplace" This class stores information of jplace file.
label_branch_pamllabel_branch_paml
maskmask
merge_treemerge_tree
NnodeNnode
NtipNtip
paml_rst-classClass "paml_rst" This class stores information of rst file...
phangorn-classClass "phangorn" This class stores ancestral sequences...
phylip-classClass "phylip" This class stores phylip tree(s)
phyPMLtreeAnno.pml
pmlToSeqpmlToSeq
print.beastListprint
r8s-classClass "r8s" This class stores output info from r8s
raxml2nwkraxml2nwk
read.basemlread.baseml
read.beastread.beast
read.codemlread.codeml
read.codeml_mlcread.codeml_mlc
read.hyphyread.hyphy
read.jplaceread.jplace
read.newickread.newick
read.nhxread.nhx
read.paml_rstread.paml_rst
read.phylipread.phylip
read.phyloTread.phyloT
read.r8sread.r8s
read.raxmlread.raxml
reexportsObjects exported from other packages
show-methodsshow method
taxa_renametaxa_rename
treedata-classClass "treedata" This class stores phylogenetic tree with...
write.jplacewrite.jplace
Bioconductor-mirror/treeio documentation built on July 21, 2017, 11:51 a.m.