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phangorn (version 1.4-0)

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

20,555

Version

1.4-0

License

GPL (>= 2)

Maintainer

Klaus Schliep

Last Published

March 27th, 2011

Functions in phangorn (1.4-0)

Laurasiatherian

Laurasiatherian data (AWCMEE)
NJ

Neighbor-Joining
phangorn-package

Phylogenetic analysis in R
ancestral.pml

Ancestral character reconstruction.
hadamard

Hadamard Matrices and Fast Hadamard Multiplication
plot.networx

Plot phylogenetic networks
lento

Lento plot
dfactorial

Arithmetic Operators
modelTest

ModelTest
consensusNet

Computes a networx object from a collection of splits.
designTree

Compute a design matrix
allTrees

Compute all trees topologies.
midpoint

Tree manipulation
bootstrap.pml

Bootstrap
SH.test

Shimodaira-Hasegawa Test
getClans

Clans, slices and clips
distanceHadamard

Distance Hadamard
pmlCluster

Stochastic Partitioning
as.splits

Splits representation of graphs and trees.
read.aa

Read Amino Acid Sequences in a File
yeast

Yeast alignment (Rokas et al.)
simSeq

Simulate sequences.
treedist

Distances between trees
pmlPart

Partition model.
splitsNetwork

Phylogenetic Network
nni

Tree rearrangements.
pml

Likelihood of a tree.
upgma

UPGMA and WPGMA
Ancestors

tree utility function
chloroplast

Chloroplast alignment
pmlMix

Phylogenetic mixture model
phyDat

Conversion among Sequence Formats
dist.hamming

Pairwise Distances from Sequences
parsimony

Parsimony tree.