Learn R Programming
⚠️There's a newer version (2.12.1) of this package.Take me there.

phangorn (version 2.0.0)

Phylogenetic Analysis in R

Description

Phylogenetic analysis in R: Estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation.

Copy Link

Version

Install

install.packages('phangorn')

Monthly Downloads

15,105

Version

2.0.0

License

GPL (>= 2)

Issues

36

Pull Requests

0

Stars

207

Forks

41

Maintainer

Klaus Schliep

Last Published

December 10th, 2015

Functions in phangorn (2.0.0)

dist.p

Pairwise Polymorphism P-Distances from DNA Sequences
modelTest

ModelTest
densiTree

Plots a densiTree.
Laurasiatherian

Laurasiatherian data (AWCMEE)
bab

Branch and bound for finding all most parsimonious trees
midpoint

Tree manipulation
pml.fit

Internal maximum likelihood functions.
chloroplast

Chloroplast alignment
plot.networx

Phylogenetic networks
ancestral.pml

Ancestral character reconstruction.
neighborNet

Computes a neighborNet from a distance matrix
dist.hamming

Pairwise Distances from Sequences
designTree

Compute a design matrix or non-negative LS
pmlPart

Partition model.
upgma

UPGMA and WPGMA
Ancestors

tree utility function
pmlCluster

Stochastic Partitioning
treedist

Distances between trees
SH.test

Shimodaira-Hasegawa Test
simSeq

Simulate sequences.
consensusNet

Computes a consensusNetwork from a list of trees Computes a networx object from a collection of splits.
distanceHadamard

Distance Hadamard
cophenetic.networx

Pairwise Distances from a Phylogenetic Network
superTree

Super Tree and Species Tree methods
as.splits

Splits representation of graphs and trees.
splitsNetwork

Phylogenetic Network
dfactorial

Arithmetic Operators
parsimony

Parsimony tree.
yeast

Yeast alignment (Rokas et al.)
allTrees

Compute all trees topologies.
lento

Lento plot
cladePar

Utility function to plot.phylo
pmlMix

Phylogenetic mixture model
pml

Likelihood of a tree.
phyDat

Conversion among Sequence Formats
hadamard

Hadamard Matrices and Fast Hadamard Multiplication
SOWH.test

Swofford-Olsen-Waddell-Hillis Test
bootstrap.pml

Bootstrap
addConfidences

Compare splits and add support values to an object
delta.score

Computes the $\delta$ score
getClans

Clans, slices and clips
phangorn-package

Phylogenetic analysis in R
read.aa

Read Amino Acid Sequences in a File
NJ

Neighbor-Joining
nni

Tree rearrangements.