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phangorn (version 1.99-13)

Phylogenetic Analysis in R

Description

Phylogenetic analysis in R: Estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation.

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Install

install.packages('phangorn')

Monthly Downloads

20,307

Version

1.99-13

License

GPL (>= 2)

Issues

Pull Requests

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Repository

https://github.com/KlausVigo/phangorn

Maintainer

Klaus Schliep

Last Published

April 7th, 2015

Functions in phangorn (1.99-13)

Chloroplast alignment

Shimodaira-Hasegawa Test

Swofford-Olsen-Waddell-Hillis Test

Clans, slices and clips

Yeast alignment (Rokas et al.)

Branch and bound for finding all most parsimonious trees

Hadamard Matrices and Fast Hadamard Multiplication

Pairwise Polymorphism P-Distances from DNA Sequences

Distances between trees

Tree rearrangements.

Likelihood of a tree.

Laurasiatherian

Laurasiatherian data (AWCMEE)

distanceHadamard

Distance Hadamard

Utility function to plot.phylo

Compute all trees topologies.

Neighbor-Joining

Stochastic Partitioning

UPGMA and WPGMA

Super Tree and Species Tree methods

Computes a neighborNet from a distance matrix

Tree manipulation

Ancestral character reconstruction.

Splits representation of graphs and trees.

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

Read Amino Acid Sequences in a File

Compute a design matrix or non-negative LS

Parsimony tree.

Simulate sequences.

Partition model.

Phylogenetic networks

Internal maximum likelihood functions.

Phylogenetic Network

Plots a densiTree.

tree utility function

phangorn-package

Phylogenetic analysis in R

Arithmetic Operators

Pairwise Distances from Sequences

Conversion among Sequence Formats

Phylogenetic mixture model