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phangorn (version 1.99-1)

Phylogenetic analysis in R

Description

Phylogenetic analysis in R (Estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, Distance methods & Hadamard conjugation)

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Version

Install

install.packages('phangorn')

Monthly Downloads

20,555

Version

1.99-1

License

GPL (>= 2)

Maintainer

Klaus Schliep

Last Published

August 21st, 2013

Functions in phangorn (1.99-1)

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

Laurasiatherian data (AWCMEE)

Branch and bound for finding all most parsimonious trees

Likelihood of a tree.

phangorn-package

Phylogenetic analysis in R

Simulate sequences.

distanceHadamard

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