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| 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 |