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