Phylogenetic analysis in R


[Package List] [Top]

Documentation for package ‘phangorn’

Help Pages

as.character.phyDat Conversion amoung Sequence Formats
as.data.frame.phyDat Conversion amoung Sequence Formats
as.phyDat.DNAbin Conversion amoung Sequence Formats
dfactorial Arithmetic Operators
dist.hamming Pairwise Distances from Sequences
dist.logDet Pairwise Distances from Sequences
distanceHadamard Distance Hadamard
fhm Hadamard Matrices and Fast Hadamard Multiplication
fitch Parsimony tree.
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
optim.parsimony Parsimony tree.
optim.pml Likelihood of a tree.
parsimony Parsimony tree.
phyDat Conversion amoung Sequence Formats
pml Likelihood of a tree.
sankoff Parsimony tree.
summary.pml Likelihood of a tree.
treedist Distances between trees
UNJ Neighbor-Joining
update.pml Likelihood of a tree.
upgma UPGMA
write.nexus.splits Hadamard Matrices and Fast Hadamard Multiplication