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phangorn (version 1.7-4)

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

21,468

Version

1.7-4

License

GPL (>= 2)

Maintainer

Klaus Schliep

Last Published

April 4th, 2013

Functions in phangorn (1.7-4)

bootstrap.pml

Bootstrap
densiTree

Plots a densiTree.
lento

Lento plot
modelTest

ModelTest
Laurasiatherian

Laurasiatherian data (AWCMEE)
read.aa

Read Amino Acid Sequences in a File
Ancestors

tree utility function
superTree

Super Tree and Species Tree methods
getClans

Clans, slices and clips
distanceHadamard

Distance Hadamard
simSeq

Simulate sequences.
dfactorial

Arithmetic Operators
pmlPart

Partition model.
SH.test

Shimodaira-Hasegawa Test
plot.networx

Plot phylogenetic networks
ancestral.pml

Ancestral character reconstruction.
consensusNet

Computes a networx object from a collection of splits.
splitsNetwork

Phylogenetic Network
pmlCluster

Stochastic Partitioning
hadamard

Hadamard Matrices and Fast Hadamard Multiplication
designTree

Compute a design matrix or non-negative LS
treedist

Distances between trees
pml

Likelihood of a tree.
parsimony

Parsimony tree.
dist.hamming

Pairwise Distances from Sequences
upgma

UPGMA and WPGMA
phangorn-package

Phylogenetic analysis in R
as.splits

Splits representation of graphs and trees.
allTrees

Compute all trees topologies.
nni

Tree rearrangements.
pmlMix

Phylogenetic mixture model
NJ

Neighbor-Joining
midpoint

Tree manipulation
yeast

Yeast alignment (Rokas et al.)
phyDat

Conversion among Sequence Formats
bab

Branch and bound for finding all most parsimonious trees
chloroplast

Chloroplast alignment