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phangorn (version 2.0.1)

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.

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Version

Install

install.packages('phangorn')

Monthly Downloads

15,105

Version

2.0.1

License

GPL (>= 2)

Issues

36

Pull Requests

0

Stars

208

Forks

41

Maintainer

Klaus Schliep

Last Published

December 14th, 2015

Functions in phangorn (2.0.1)

chloroplast

Chloroplast alignment
NJ

Neighbor-Joining
SOWH.test

Swofford-Olsen-Waddell-Hillis Test
designTree

Compute a design matrix or non-negative LS
lento

Lento plot
parsimony

Parsimony tree.
dist.hamming

Pairwise Distances from Sequences
dfactorial

Arithmetic Operators
nni

Tree rearrangements.
SH.test

Shimodaira-Hasegawa Test
superTree

Super Tree and Species Tree methods
phyDat

Conversion among Sequence Formats
phangorn-package

Phylogenetic analysis in R
as.splits

Splits representation of graphs and trees.
simSeq

Simulate sequences.
getClans

Clans, slices and clips
allTrees

Compute all trees topologies.
ancestral.pml

Ancestral character reconstruction.
delta.score

Computes the $\delta$ score
consensusNet

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

Partition model.
splitsNetwork

Phylogenetic Network
midpoint

Tree manipulation
neighborNet

Computes a neighborNet from a distance matrix
pmlMix

Phylogenetic mixture model
pml

Likelihood of a tree.
upgma

UPGMA and WPGMA
Ancestors

tree utility function
plot.networx

Phylogenetic networks
pml.fit

Internal maximum likelihood functions.
Laurasiatherian

Laurasiatherian data (AWCMEE)
bab

Branch and bound for finding all most parsimonious trees
dist.p

Pairwise Polymorphism P-Distances from DNA Sequences
distanceHadamard

Distance Hadamard
addConfidences

Compare splits and add support values to an object
cladePar

Utility function to plot.phylo
cophenetic.networx

Pairwise Distances from a Phylogenetic Network
bootstrap.pml

Bootstrap
pmlCluster

Stochastic Partitioning
read.aa

Read Amino Acid Sequences in a File
densiTree

Plots a densiTree.
hadamard

Hadamard Matrices and Fast Hadamard Multiplication
treedist

Distances between trees
modelTest

ModelTest
yeast

Yeast alignment (Rokas et al.)