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phangorn (version 1.6-3)

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

24,436

Version

1.6-3

License

GPL (>= 2)

Maintainer

Klaus Schliep

Last Published

July 1st, 2012

Functions in phangorn (1.6-3)

Ancestors

tree utility function
pmlPart

Partition model.
splitsNetwork

Phylogenetic Network
chloroplast

Chloroplast alignment
midpoint

Tree manipulation
parsimony

Parsimony tree.
pml

Likelihood of a tree.
pmlMix

Phylogenetic mixture model
treedist

Distances between trees
dist.hamming

Pairwise Distances from Sequences
as.splits

Splits representation of graphs and trees.
ancestral.pml

Ancestral character reconstruction.
distanceHadamard

Distance Hadamard
yeast

Yeast alignment (Rokas et al.)
pmlCluster

Stochastic Partitioning
allTrees

Compute all trees topologies.
getClans

Clans, slices and clips
nni

Tree rearrangements.
modelTest

ModelTest
hadamard

Hadamard Matrices and Fast Hadamard Multiplication
simSeq

Simulate sequences.
bab

Branch and bound for finding all most parsimonious trees
phyDat

Conversion among Sequence Formats
designTree

Compute a design matrix or non-negative LS
plot.networx

Plot phylogenetic networks
NJ

Neighbor-Joining
bootstrap.pml

Bootstrap
phangorn-package

Phylogenetic analysis in R
Laurasiatherian

Laurasiatherian data (AWCMEE)
upgma

UPGMA and WPGMA
lento

Lento plot
dfactorial

Arithmetic Operators
SH.test

Shimodaira-Hasegawa Test
consensusNet

Computes a networx object from a collection of splits.
read.aa

Read Amino Acid Sequences in a File