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phangorn (version 1.0-0)

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

19,890

Version

1.0-0

License

GPL (>= 2)

Maintainer

Klaus Schliep

Last Published

March 18th, 2010

Functions in phangorn (1.0-0)

Neighbor-Joining

Arithmetic Operators

Chloroplast alignment

distanceHadamard

Distance Hadamard

Shimodaira-Hasegawa Test

Tree rearrangements.

Hadamard Matrices and Fast Hadamard Multiplication

tree utility function

Likelihood of a tree.

Compute all trees topologies.

Compute a design matrix

Conversion among Sequence Formats

Parsimony tree.

Splits representation of graphs and trees

Simulate sequences.

Phylogenetic Network

Yeast alignment (Rokas et al.)

Phylogenetic mixture model

Partition model.

Stochastic Partitioning

Laurasiatherian

Laurasiatherian data (AWCMEE)

Distances between trees

Read Amino Acid Sequences in a File

Pairwise Distances from Sequences