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phangorn (version 1.99-12)

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

20,555

Version

1.99-12

License

GPL (>= 2)

Issues

Pull Requests

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Repository

https://github.com/KlausVigo/phangorn

Maintainer

Klaus Schliep

Last Published

February 13th, 2015

Functions in phangorn (1.99-12)

Laurasiatherian

Laurasiatherian data (AWCMEE)

Swofford-Olsen-Waddell-Hillis Test

Splits representation of graphs and trees.

Pairwise Distances from Sequences

Arithmetic Operators

Compute a design matrix or non-negative LS

Compute all trees topologies.

Plots a densiTree.

Conversion among Sequence Formats

Phylogenetic networks

Yeast alignment (Rokas et al.)

UPGMA and WPGMA

tree utility function

Neighbor-Joining

distanceHadamard

Distance Hadamard

Branch and bound for finding all most parsimonious trees

Computes a neighborNet from a distance matrix

Utility function to plot.phylo

Shimodaira-Hasegawa Test

Super Tree and Species Tree methods

Tree manipulation

Parsimony tree.

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

Phylogenetic mixture model

Stochastic Partitioning

Phylogenetic Network

Hadamard Matrices and Fast Hadamard Multiplication

Distances between trees

Ancestral character reconstruction.

Likelihood of a tree.

Tree rearrangements.

Chloroplast alignment

Simulate sequences.

Read Amino Acid Sequences in a File

Partition model.

Pairwise Polymorphism P-Distances from DNA Sequences

Internal maximum likelihood functions.

Clans, slices and clips

phangorn-package

Phylogenetic analysis in R