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.) |