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phangorn (version 0.99-4)

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

0.99-4

License

GPL (>= 2)

Maintainer

Klaus Schliep

Last Published

November 27th, 2009

Functions in phangorn (0.99-4)

pml

Likelihood of a tree.
hadamard

Hadamard Matrices and Fast Hadamard Multiplication
designTree

Compute a design matrix
simSeq

Simulate sequences.
dfactorial

Arithmetic Operators
upgma

UPGMA
splitsNetwork

Phylogenetic Network
pmlCluster

Stochastic Partitioning
yeast

Yeast alignment (Rokas et al.)
SH.test

Shimodaira-Hasegawa Test
NJ

Neighbor-Joining
read.aa

Read Amino Acid Sequences in a File
treedist

Distances between trees
distanceHadamard

Distance Hadamard
phyDat

Conversion amoung Sequence Formats
chloroplast

Chloroplast alignment
allTrees

Compute all trees topologies.
pmlMix

Phylogenetic mixture model
bootstrap.pml

Bootstrap
parsimony

Parsimony tree.
pmlPart

Partition model.
dist.hamming

Pairwise Distances from Sequences
nni

Tree rearrangements.
Laurasiatherian

Laurasiatherian data (AWCMEE)