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phangorn (version 1.3-1)

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

17,645

Version

1.3-1

License

GPL (>= 2)

Maintainer

Klaus Schliep

Last Published

February 14th, 2011

Functions in phangorn (1.3-1)

SH.test

Shimodaira-Hasegawa Test
as.splits

Splits representation of graphs and trees.
NJ

Neighbor-Joining
allTrees

Compute all trees topologies.
designTree

Compute a design matrix
Laurasiatherian

Laurasiatherian data (AWCMEE)
bootstrap.pml

Bootstrap
pmlMix

Phylogenetic mixture model
distanceHadamard

Distance Hadamard
ancestral.pml

Ancestral character reconstruction.
hadamard

Hadamard Matrices and Fast Hadamard Multiplication
pmlPart

Partition model.
splitsNetwork

Phylogenetic Network
treedist

Distances between trees
lento

Lento plot
nni

Tree rearrangements.
modelTest

ModelTest
getClans

Clans, slices and clips
parsimony

Parsimony tree.
dfactorial

Arithmetic Operators
phyDat

Conversion among Sequence Formats
yeast

Yeast alignment (Rokas et al.)
dist.hamming

Pairwise Distances from Sequences
pml

Likelihood of a tree.
phangorn-package

Phylogenetic analysis in R
simSeq

Simulate sequences.
upgma

UPGMA and WPGMA
chloroplast

Chloroplast alignment
pmlCluster

Stochastic Partitioning
midpoint

Tree manipulation
Ancestors

tree utility function
read.aa

Read Amino Acid Sequences in a File