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