allSitePattern | Conversion among Sequence Formats |
allTrees | Compute all trees topologies. |
Ancestors | tree utility function |
as.character.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 |
bootstrap.phyDat | Bootstrap |
bootstrap.pml | Bootstrap |
Children | tree utility function |
chloroplast | Chloroplast alignment |
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 |
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. |
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 |
treedist | Distances between trees |
UNJ | Neighbor-Joining |
upgma | UPGMA |
write.nexus.splits | Hadamard Matrices and Fast Hadamard Multiplication |
write.phyDat | Conversion among Sequence Formats |
yeast | Yeast alignment (Rokas et al.) |
[.phyDat | Conversion among Sequence Formats |