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phangorn (version 1.99-9)

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

1.99-9

License

GPL (>= 2)

Issues

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Repository

https://github.com/KlausVigo/phangorn

Maintainer

Klaus Schliep

Last Published

October 9th, 2014

Functions in phangorn (1.99-9)

Chloroplast alignment

Phylogenetic mixture model

Conversion among Sequence Formats

Arithmetic Operators

Shimodaira-Hasegawa Test

Tree manipulation

tree utility function

phangorn-package

Phylogenetic analysis in R

Tree rearrangements.

Yeast alignment (Rokas et al.)

Swofford-Olsen-Waddell-Hillis Test

Ancestral character reconstruction.

Splits representation of graphs and trees.

Phylogenetic networks

Internal maximum likelihood functions.

Read Amino Acid Sequences in a File

Branch and bound for finding all most parsimonious trees

Hadamard Matrices and Fast Hadamard Multiplication

Parsimony tree.

Partition model.

Pairwise Polymorphism P-Distances from DNA Sequences

Clans, slices and clips

Pairwise Distances from Sequences

Plots a densiTree.

Stochastic Partitioning

Super Tree and Species Tree methods

Likelihood of a tree.

UPGMA and WPGMA

Distances between trees

distanceHadamard

Distance Hadamard

Phylogenetic Network

Compute a design matrix or non-negative LS

Utility function to plot.phylo

Neighbor-Joining

Laurasiatherian

Laurasiatherian data (AWCMEE)

Compute all trees topologies.

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

Simulate sequences.