Phylogenetic analysis in R

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Documentation for package ‘phangorn’

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allSitePattern Conversion amoung Sequence Formats
allTrees Compute all trees topologies and nearest neighbor interchange.
as.character.phyDat Conversion amoung Sequence Formats
as.data.frame.phyDat Conversion amoung Sequence Formats
as.phyDat.DNAbin Conversion amoung Sequence Formats
chloroplast Chloroplast alignment
designSplits Compute a design matrix
designTree Compute a design matrix
dfactorial Arithmetic Operators
dist.hamming Pairwise Distances from Sequences
dist.logDet Pairwise Distances from Sequences
dist.ml Pairwise Distances from Sequences
distanceHadamard Distance Hadamard
fhm Hadamard Matrices and Fast Hadamard Multiplication
fitch Parsimony tree.
getEdgeLength Compute a design matrix
h2st Hadamard Matrices and Fast Hadamard Multiplication
h4st Hadamard Matrices and Fast Hadamard Multiplication
hadamard Hadamard Matrices and Fast Hadamard Multiplication
Laurasiatherian Laurasiatherian data (AWCMEE)
ldfactorial Arithmetic Operators
NJ Neighbor-Joining
nni Compute all trees topologies and nearest neighbor interchange.
optim.parsimony Parsimony tree.
optim.pml Likelihood of a tree.
parsimony Parsimony tree.
phyDat Conversion amoung Sequence Formats
pml Likelihood of a tree.
pmlCluster Stochastic Partitioning
pmlMix Phylogenetic mixture model
pmlPart Partition model.
pmlPen Phylogenetic mixture model
PNJ Parsimony tree.
read.aa Read Amino Acid Sequences in a File
sankoff Parsimony tree.
splitsNetwork Phylogenetic Network
treedist Distances between trees
UNJ Neighbor-Joining
upgma UPGMA
write.nexus.splits Hadamard Matrices and Fast Hadamard Multiplication
yeast Yeast alignment (Rokas et al.)