Phylogenetic Reconstruction and Analysis

addConfidences | Compare splits and add support values to an object |

add.tips | Add tips to a tree |

allTrees | Compute all trees topologies. |

Ancestors | tree utility function |

ancestral.pml | Ancestral character reconstruction. |

as.networx | Phylogenetic networks |

as.splits | Splits representation of graphs and trees. |

bab | Branch and bound for finding all most parsimonious trees |

bootstrap.pml | Bootstrap |

chloroplast | Chloroplast alignment |

CI | Consistency Index and Retention Index |

cladePar | Utility function to plot.phylo |

coalSpeciesTree | Species Tree |

consensusNet | Computes a consensusNetwork from a list of trees Computes a... |

cophenetic.networx | Pairwise Distances from a Phylogenetic Network |

delta.score | Computes the delta score |

densiTree | Plots a densiTree. |

designTree | Compute a design matrix or non-negative LS |

dfactorial | Arithmetic Operators |

distanceHadamard | Distance Hadamard |

dist.hamming | Pairwise Distances from Sequences |

dist.p | Pairwise Polymorphism P-Distances from DNA Sequences |

getClans | Clans, slices and clips |

hadamard | Hadamard Matrices and Fast Hadamard Multiplication |

identify.networx | Identify splits in a network |

Laurasiatherian | Laurasiatherian data (AWCMEE) |

lento | Lento plot |

mast | Maximum agreement subtree |

maxCladeCred | Maximum clade credibility tree |

midpoint | Tree manipulation |

modelTest | ModelTest |

neighborNet | Computes a neighborNet from a distance matrix |

NJ | Neighbor-Joining |

nni | Tree rearrangements. |

parsimony | Parsimony tree. |

phangorn-internal | Internal phangorn Functions |

phangorn-package | Phylogenetic analysis in R |

phyDat | Conversion among Sequence Formats |

pml | Likelihood of a tree. |

pmlCluster | Stochastic Partitioning |

pml.fit | Internal maximum likelihood functions. |

pmlMix | Phylogenetic mixture model |

pmlPart | Partition model. |

read.aa | Read Amino Acid Sequences in a File |

read.nexus.splits | Function to import and export splits and networks |

SH.test | Shimodaira-Hasegawa Test |

simSeq | Simulate sequences. |

SOWH.test | Swofford-Olsen-Waddell-Hillis Test |

splitsNetwork | Phylogenetic Network |

superTree | Super Tree methods |

treedist | Distances between trees |

upgma | UPGMA and WPGMA |

writeDist | Writing and reading distances in phylip and nexus format |

yeast | Yeast alignment (Rokas et al.) |

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