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phangorn (version 1.99-5)

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

20,307

Version

1.99-5

License

GPL (>= 2)

Maintainer

Klaus Schliep

Last Published

January 2nd, 2014

Functions in phangorn (1.99-5)

designTree

Compute a design matrix or non-negative LS
nni

Tree rearrangements.
bab

Branch and bound for finding all most parsimonious trees
ancestral.pml

Ancestral character reconstruction.
modelTest

ModelTest
bootstrap.pml

Bootstrap
read.aa

Read Amino Acid Sequences in a File
simSeq

Simulate sequences.
phangorn-package

Phylogenetic analysis in R
pml

Likelihood of a tree.
plot.networx

Plot phylogenetic networks
chloroplast

Chloroplast alignment
pmlCluster

Stochastic Partitioning
SH.test

Shimodaira-Hasegawa Test
superTree

Super Tree and Species Tree methods
midpoint

Tree manipulation
dist.p

Pairwise Polymorphism P-Distances from DNA Sequences
consensusNet

Computes a networx object from a collection of splits.
pmlMix

Phylogenetic mixture model
dist.hamming

Pairwise Distances from Sequences
hadamard

Hadamard Matrices and Fast Hadamard Multiplication
densiTree

Plots a densiTree.
lento

Lento plot
treedist

Distances between trees
NJ

Neighbor-Joining
yeast

Yeast alignment (Rokas et al.)
allTrees

Compute all trees topologies.
distanceHadamard

Distance Hadamard
Ancestors

tree utility function
as.splits

Splits representation of graphs and trees.
Laurasiatherian

Laurasiatherian data (AWCMEE)
dfactorial

Arithmetic Operators
upgma

UPGMA and WPGMA
splitsNetwork

Phylogenetic Network
phyDat

Conversion among Sequence Formats
pmlPart

Partition model.
getClans

Clans, slices and clips
pml.fit

Internal maximum likelihood functions.
parsimony

Parsimony tree.