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