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phangorn (version 0.0-5)

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

0.0-5

License

GPL (>=2)

Maintainer

Klaus Schliep

Last Published

September 17th, 2024

Functions in phangorn (0.0-5)

NJ

Neighbor-Joining
dfactorial

Arithmetic Operators
allTrees

Compute all trees topologies and nearest neighbor interchange.
pmlPart

Partition model.
phyDat

Conversion amoung Sequence Formats
dist.hamming

Pairwise Distances from Sequences
designTree

Compute a design matrix
pml

Likelihood of a tree.
pmlCluster

Stochastic Partitioning
Laurasiatherian

Laurasiatherian data (AWCMEE)
pmlMix

Phylogenetic mixture model
upgma

UPGMA
distanceHadamard

Distance Hadamard
parsimony

Parsimony tree.
splitsNetwork

Phylogenetic Network
yeast

Yeast alignment (Rokas et al.)
read.aa

Read Amino Acid Sequences in a File
hadamard

Hadamard Matrices and Fast Hadamard Multiplication
chloroplast

Chloroplast alignment
treedist

Distances between trees