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phangorn (version 1.0-2)

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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Version

Install

install.packages('phangorn')

Monthly Downloads

20,307

Version

1.0-2

License

GPL (>= 2)

Maintainer

Klaus Schliep

Last Published

May 16th, 2010

Functions in phangorn (1.0-2)

Compute all trees topologies.

Pairwise Distances from Sequences

Splits representation of graphs and trees.

Likelihood of a tree.

Tree rearrangements.

Stochastic Partitioning

Yeast alignment (Rokas et al.)

Simulate sequences.

Chloroplast alignment

Arithmetic Operators

distanceHadamard

Distance Hadamard

Laurasiatherian

Laurasiatherian data (AWCMEE)

tree utility function

Hadamard Matrices and Fast Hadamard Multiplication

Partition model.

Shimodaira-Hasegawa Test

Phylogenetic Network

Parsimony tree.

Phylogenetic mixture model

Distances between trees

Conversion among Sequence Formats

Read Amino Acid Sequences in a File

Compute a design matrix

UPGMA and WPGMA

Ancestral character reconstruction.

Neighbor-Joining