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phangorn (version 1.5-1)

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

15,105

Version

1.5-1

License

GPL (>= 2)

Maintainer

Klaus Schliep

Last Published

December 13th, 2011

Functions in phangorn (1.5-1)

chloroplast

Chloroplast alignment
getClans

Clans, slices and clips
lento

Lento plot
bab

Branch and bound for finding all most parsimonious trees
dfactorial

Arithmetic Operators
distanceHadamard

Distance Hadamard
NJ

Neighbor-Joining
modelTest

ModelTest
nni

Tree rearrangements.
consensusNet

Computes a networx object from a collection of splits.
Ancestors

tree utility function
parsimony

Parsimony tree.
SH.test

Shimodaira-Hasegawa Test
bootstrap.pml

Bootstrap
pmlCluster

Stochastic Partitioning
as.splits

Splits representation of graphs and trees.
upgma

UPGMA and WPGMA
designTree

Compute a design matrix or non-negative LS
midpoint

Tree manipulation
Laurasiatherian

Laurasiatherian data (AWCMEE)
pmlMix

Phylogenetic mixture model
dist.hamming

Pairwise Distances from Sequences
treedist

Distances between trees
allTrees

Compute all trees topologies.
ancestral.pml

Ancestral character reconstruction.
plot.networx

Plot phylogenetic networks
yeast

Yeast alignment (Rokas et al.)
splitsNetwork

Phylogenetic Network
phyDat

Conversion among Sequence Formats
hadamard

Hadamard Matrices and Fast Hadamard Multiplication
phangorn-package

Phylogenetic analysis in R
simSeq

Simulate sequences.
read.aa

Read Amino Acid Sequences in a File
pmlPart

Partition model.
pml

Likelihood of a tree.