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| 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. |
| 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.) |