Phylogenetic analysis in R


[Up] [Top]

Documentation for package ‘phangorn’ version 1.0-2

Help Pages

acgt2ry Conversion among Sequence Formats
allSitePattern Conversion among Sequence Formats
allTrees Compute all trees topologies.
Ancestors tree utility function
ancestral.pars Ancestral character reconstruction.
ancestral.pml Ancestral character reconstruction.
as.character.phyDat Conversion among Sequence Formats
as.data.frame.phyDat Conversion among Sequence Formats
as.DNAbin.phyDat Conversion among Sequence Formats
as.phyDat Conversion among Sequence Formats
as.phyDat.DNAbin Conversion among Sequence Formats
as.splits Splits representation of graphs and trees.
as.splits.multiPhylo Splits representation of graphs and trees.
as.splits.phylo Splits representation of graphs and trees.
bootstrap.phyDat Bootstrap
bootstrap.pml Bootstrap
Children tree utility function
chloroplast Chloroplast alignment
compatible Splits representation of graphs and trees.
Descendants tree utility function
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.
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
lento Lento plot
modelTest ModelTest
NJ Neighbor-Joining
nni Tree rearrangements.
optim.parsimony Parsimony tree.
optim.pml Likelihood of a tree.
pace Parsimony tree.
parsimony Parsimony tree.
phyDat Conversion among Sequence Formats
plotBS Bootstrap
pml Likelihood of a tree.
pml.control 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
read.phyDat Conversion among Sequence Formats
RF.dist Distances between trees
rNNI Tree rearrangements.
rSPR Tree rearrangements.
sankoff Parsimony tree.
SH.test Shimodaira-Hasegawa Test
Siblings tree utility function
simSeq Simulate sequences.
splitsNetwork Phylogenetic Network
subset.phyDat Conversion among Sequence Formats
treedist Distances between trees
UNJ Neighbor-Joining
upgma UPGMA and WPGMA
wpgma UPGMA and WPGMA
write.nexus.splits Hadamard Matrices and Fast Hadamard Multiplication
write.phyDat Conversion among Sequence Formats
yeast Yeast alignment (Rokas et al.)