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phangorn (version 0.99-3)

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

24,436

Version

0.99-3

License

GPL (>= 2)

Maintainer

Klaus Schliep

Last Published

October 30th, 2009

Functions in phangorn (0.99-3)

dfactorial

Arithmetic Operators
designTree

Compute a design matrix
bootstrap.pml

Bootstrap
pmlMix

Phylogenetic mixture model
simSeq

Simulate sequences.
upgma

UPGMA
parsimony

Parsimony tree.
Laurasiatherian

Laurasiatherian data (AWCMEE)
NJ

Neighbor-Joining
SH.test

Shimodaira-Hasegawa Test
chloroplast

Chloroplast alignment
read.aa

Read Amino Acid Sequences in a File
treedist

Distances between trees
allTrees

Compute all trees topologies.
nni

Tree rearrangements.
splitsNetwork

Phylogenetic Network
hadamard

Hadamard Matrices and Fast Hadamard Multiplication
dist.hamming

Pairwise Distances from Sequences
distanceHadamard

Distance Hadamard
phyDat

Conversion amoung Sequence Formats
pmlCluster

Stochastic Partitioning
pmlPart

Partition model.
yeast

Yeast alignment (Rokas et al.)
pml

Likelihood of a tree.