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phangorn (version 1.99-11)

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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Install

install.packages('phangorn')

Monthly Downloads

20,307

Version

1.99-11

License

GPL (>= 2)

Issues

Pull Requests

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Repository

https://github.com/KlausVigo/phangorn

Maintainer

Klaus Schliep

Last Published

November 11th, 2014

Functions in phangorn (1.99-11)

Laurasiatherian

Laurasiatherian data (AWCMEE)

Shimodaira-Hasegawa Test

distanceHadamard

Distance Hadamard

Hadamard Matrices and Fast Hadamard Multiplication

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

tree utility function

Phylogenetic mixture model

Neighbor-Joining

Yeast alignment (Rokas et al.)

Pairwise Polymorphism P-Distances from DNA Sequences

Stochastic Partitioning

Ancestral character reconstruction.

Simulate sequences.

Branch and bound for finding all most parsimonious trees

Compute a design matrix or non-negative LS

Likelihood of a tree.

UPGMA and WPGMA

Arithmetic Operators

Distances between trees

Clans, slices and clips

Read Amino Acid Sequences in a File

Utility function to plot.phylo

Swofford-Olsen-Waddell-Hillis Test

Partition model.

phangorn-package

Phylogenetic analysis in R

Parsimony tree.

Phylogenetic Network

Splits representation of graphs and trees.

Compute all trees topologies.

Tree rearrangements.

Tree manipulation

Pairwise Distances from Sequences

Chloroplast alignment

Internal maximum likelihood functions.

Conversion among Sequence Formats

Phylogenetic networks

Plots a densiTree.

Super Tree and Species Tree methods