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