Learn R Programming

⚠️There's a newer version (2.12.1) of this package.Take me there.

phangorn (version 1.99-8)

Phylogenetic analysis in R

Description

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

Copy Link

Version

Install

install.packages('phangorn')

Monthly Downloads

20,307

Version

1.99-8

License

GPL (>= 2)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/KlausVigo/phangorn

Maintainer

Klaus Schliep

Last Published

October 7th, 2014

Functions in phangorn (1.99-8)

phangorn-package

Phylogenetic analysis in R

Conversion among Sequence Formats

Tree manipulation

Phylogenetic mixture model

distanceHadamard

Distance Hadamard

Laurasiatherian

Laurasiatherian data (AWCMEE)

Likelihood of a tree.

Shimodaira-Hasegawa Test

UPGMA and WPGMA

Compute all trees topologies.

Compute a design matrix or non-negative LS

Pairwise Polymorphism P-Distances from DNA Sequences

Ancestral character reconstruction.

Chloroplast alignment

Neighbor-Joining

Clans, slices and clips

Utility function to plot.phylo

Internal maximum likelihood functions.

Phylogenetic networks

Branch and bound for finding all most parsimonious trees

Pairwise Distances from Sequences

Arithmetic Operators

tree utility function

Distances between trees

Phylogenetic Network

Computes a conensusNetwork from a list of trees Computes a networx object from a collection of splits.

Stochastic Partitioning

Partition model.

Yeast alignment (Rokas et al.)

Splits representation of graphs and trees.

Parsimony tree.

Hadamard Matrices and Fast Hadamard Multiplication

Plots a densiTree.

Tree rearrangements.

Read Amino Acid Sequences in a File

Simulate sequences.

Super Tree and Species Tree methods

Swofford-Olsen-Waddell-Hillis Test