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phangorn (version 2.0.2)

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

20,307

Version

2.0.2

License

GPL (>= 2)

Issues

29

Pull Requests

0

Stars

214

Forks

41

Maintainer

Klaus Schliep

Last Published

January 22nd, 2016

Functions in phangorn (2.0.2)

bootstrap.pml

Bootstrap
dist.p

Pairwise Polymorphism P-Distances from DNA Sequences
nni

Tree rearrangements.
distanceHadamard

Distance Hadamard
allTrees

Compute all trees topologies.
NJ

Neighbor-Joining
cladePar

Utility function to plot.phylo
superTree

Super Tree and Species Tree methods
ancestral.pml

Ancestral character reconstruction.
dfactorial

Arithmetic Operators
hadamard

Hadamard Matrices and Fast Hadamard Multiplication
read.aa

Read Amino Acid Sequences in a File
phyDat

Conversion among Sequence Formats
dist.hamming

Pairwise Distances from Sequences
plot.networx

Phylogenetic networks
pml.fit

Internal maximum likelihood functions.
simSeq

Simulate sequences.
upgma

UPGMA and WPGMA
as.splits

Splits representation of graphs and trees.
pmlMix

Phylogenetic mixture model
parsimony

Parsimony tree.
delta.score

Computes the $\delta$ score
midpoint

Tree manipulation
neighborNet

Computes a neighborNet from a distance matrix
chloroplast

Chloroplast alignment
SH.test

Shimodaira-Hasegawa Test
densiTree

Plots a densiTree.
lento

Lento plot
modelTest

ModelTest
getClans

Clans, slices and clips
pml

Likelihood of a tree.
treedist

Distances between trees
consensusNet

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

tree utility function
addConfidences

Compare splits and add support values to an object
cophenetic.networx

Pairwise Distances from a Phylogenetic Network
pmlCluster

Stochastic Partitioning
pmlPart

Partition model.
splitsNetwork

Phylogenetic Network
phangorn-package

Phylogenetic analysis in R
yeast

Yeast alignment (Rokas et al.)
designTree

Compute a design matrix or non-negative LS
bab

Branch and bound for finding all most parsimonious trees
SOWH.test

Swofford-Olsen-Waddell-Hillis Test
Laurasiatherian

Laurasiatherian data (AWCMEE)