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phangorn (version 1.99.14)

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

17,645

Version

1.99.14

License

GPL (>= 2)

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Repository

https://github.com/KlausVigo/phangorn

Maintainer

Klaus Schliep

Last Published

July 9th, 2015

Functions in phangorn (1.99.14)

Compute all trees topologies.

Compute a design matrix or non-negative LS

Splits representation of graphs and trees.

Phylogenetic Network

Pairwise Distances from Sequences

Neighbor-Joining

Swofford-Olsen-Waddell-Hillis Test

Tree rearrangements.

Likelihood of a tree.

Super Tree and Species Tree methods

Phylogenetic mixture model

Read Amino Acid Sequences in a File

Yeast alignment (Rokas et al.)

Computes a neighborNet from a distance matrix

tree utility function

UPGMA and WPGMA

Chloroplast alignment

Tree manipulation

Conversion among Sequence Formats

Hadamard Matrices and Fast Hadamard Multiplication

Arithmetic Operators

Phylogenetic networks

Internal maximum likelihood functions.

phangorn-package

Phylogenetic analysis in R

Utility function to plot.phylo

Partition model.

distanceHadamard

Distance Hadamard

Laurasiatherian

Laurasiatherian data (AWCMEE)

Branch and bound for finding all most parsimonious trees

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

Shimodaira-Hasegawa Test

Plots a densiTree.

Distances between trees

Parsimony tree.

Pairwise Polymorphism P-Distances from DNA Sequences

Stochastic Partitioning

Ancestral character reconstruction.

Simulate sequences.

Clans, slices and clips