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