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phangorn (version 1.5-0)

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

21,468

Version

1.5-0

License

GPL (>= 2)

Maintainer

Klaus Schliep

Last Published

December 10th, 2011

Functions in phangorn (1.5-0)

Pairwise Distances from Sequences

phangorn-package

Phylogenetic analysis in R

tree utility function

Branch and bound for finding all most parsimonious trees

distanceHadamard

Distance Hadamard

Splits representation of graphs and trees.

Tree rearrangements.

Compute a design matrix or non-negative LS

Neighbor-Joining

UPGMA and WPGMA

Hadamard Matrices and Fast Hadamard Multiplication

Partition model.

Computes a networx object from a collection of splits.

Compute all trees topologies.

Clans, slices and clips

Tree manipulation

Laurasiatherian

Laurasiatherian data (AWCMEE)

Simulate sequences.

Phylogenetic Network

Ancestral character reconstruction.

Arithmetic Operators

Shimodaira-Hasegawa Test

Chloroplast alignment

Read Amino Acid Sequences in a File

Parsimony tree.

Likelihood of a tree.

Phylogenetic mixture model

Conversion among Sequence Formats

Plot phylogenetic networks

Stochastic Partitioning

Distances between trees

Yeast alignment (Rokas et al.)