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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 |
| 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 |
| logLik.pml | Likelihood of a tree. |
| 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. |
| predict.pml | Likelihood of a tree. |
| print.phyDat | Conversion amoung Sequence Formats |
| print.pml | Likelihood of a tree. |
| print.summary.pml | Likelihood of a tree. |
| print.treedist | Distances between trees |
| sankoff | Parsimony tree. |
| seq2split | Hadamard Matrices and Fast Hadamard Multiplication |
| split2seq | Hadamard Matrices and Fast Hadamard Multiplication |
| summary.pml | Likelihood of a tree. |
| treedist | Distances between trees |
| UNJ | Neighbor-Joining |
| upgma | UPGMA |
| vcov.pml | Likelihood of a tree. |
| write.nexus.splits | Hadamard Matrices and Fast Hadamard Multiplication |