Chloroplast alignment
Shimodaira-Hasegawa Test
Swofford-Olsen-Waddell-Hillis Test
Clans, slices and clips
Yeast alignment (Rokas et al.)
Branch and bound for finding all most parsimonious trees
Hadamard Matrices and Fast Hadamard Multiplication
Pairwise Polymorphism P-Distances from DNA Sequences
Distances between trees
Tree rearrangements.
Bootstrap
Likelihood of a tree.
Laurasiatherian data (AWCMEE)
Distance Hadamard
Utility function to plot.phylo
Compute all trees topologies.
Neighbor-Joining
Stochastic Partitioning
UPGMA and WPGMA
Super Tree and Species Tree methods
Computes a neighborNet from a distance matrix
Tree manipulation
Ancestral character reconstruction.
Splits representation of graphs and trees.
Computes a consensusNetwork from a list of trees
Computes a networx
object from a collection of splits.
Read Amino Acid Sequences in a File
Compute a design matrix or non-negative LS
Parsimony tree.
Simulate sequences.
Partition model.
Phylogenetic networks
Internal maximum likelihood functions.
Phylogenetic Network
Plots a densiTree.
tree utility function
Phylogenetic analysis in R
Arithmetic Operators
Pairwise Distances from Sequences
Conversion among Sequence Formats
Lento plot
ModelTest
Phylogenetic mixture model