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