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phangorn (version 2.0.3)

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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Install

install.packages('phangorn')

Monthly Downloads

20,555

Version

2.0.3

License

GPL (>= 2)

Issues

36

Pull Requests

0

Stars

207

Forks

40

Maintainer

Klaus Schliep

Last Published

April 30th, 2016

Functions in phangorn (2.0.3)

Laurasiatherian

Laurasiatherian data (AWCMEE)
Ancestors

tree utility function
delta.score

Computes the $\delta$ score
cophenetic.networx

Pairwise Distances from a Phylogenetic Network
phangorn-package

Phylogenetic analysis in R
splitsNetwork

Phylogenetic Network
as.splits

Splits representation of graphs and trees.
allTrees

Compute all trees topologies.
SH.test

Shimodaira-Hasegawa Test
dist.hamming

Pairwise Distances from Sequences
simSeq

Simulate sequences.
designTree

Compute a design matrix or non-negative LS
lento

Lento plot
hadamard

Hadamard Matrices and Fast Hadamard Multiplication
pml.fit

Internal maximum likelihood functions.
pmlCluster

Stochastic Partitioning
phyDat

Conversion among Sequence Formats
addConfidences

Compare splits and add support values to an object
cladePar

Utility function to plot.phylo
pml

Likelihood of a tree.
consensusNet

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

Tree manipulation
bootstrap.pml

Bootstrap
bab

Branch and bound for finding all most parsimonious trees
parsimony

Parsimony tree.
pmlPart

Partition model.
upgma

UPGMA and WPGMA
NJ

Neighbor-Joining
chloroplast

Chloroplast alignment
dist.p

Pairwise Polymorphism P-Distances from DNA Sequences
neighborNet

Computes a neighborNet from a distance matrix
pmlMix

Phylogenetic mixture model
maxCladeCred

Maximum clade credibility tree
modelTest

ModelTest
plot.networx

Phylogenetic networks
yeast

Yeast alignment (Rokas et al.)
treedist

Distances between trees
superTree

Super Tree and Species Tree methods
densiTree

Plots a densiTree.
ancestral.pml

Ancestral character reconstruction.
dfactorial

Arithmetic Operators
nni

Tree rearrangements.
getClans

Clans, slices and clips
SOWH.test

Swofford-Olsen-Waddell-Hillis Test
read.aa

Read Amino Acid Sequences in a File
distanceHadamard

Distance Hadamard