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