phangorn v2.5.5

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Phylogenetic Reconstruction and Analysis

Package contains methods for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation. Allows to compare trees, models selection and offers visualizations for trees and split networks.

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phangorn

phangorn is a package for phylogenetic reconstruction and analysis in the R language. phangorn offers the possibility of reconstructing phylogenies with distance based methods, maximum parsimony or maximum likelihood (ML) and performing Hadamard conjugation. Extending the general ML framework, this package provides the possibility of estimating mixture and partition models. Furthermore, phangorn offers several functions for comparing trees, phylogenetic models or splits, simulating character data and performing congruence analyses.

You can install

  • the latest released version install.packages("phangorn")
  • the latest development version remotes::install_github("KlausVigo/phangorn")

To install the development version you may need to install the Biostrings and seqLogo package from bioconductor first:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(c("Biostrings", "seqLogo"))

Also the development version usually depends on tha latest ape development version and information to download can be found here. Additionally you may need to install on windows Rtools and on mac XCode and GFortran.

If you use phangorn please cite:

Schliep K.P. 2011. phangorn: phylogenetic analysis in R. Bioinformatics, 27(4) 592-593

License

phangorn is licensed under the GPLv2.

Functions in phangorn

Name Description
allSplits Splits representation of graphs and trees.
ldfactorial Arithmetic Operators
nni Tree rearrangements.
neighborNet Computes a neighborNet from a distance matrix
designTree Compute a design matrix or non-negative LS
acctran Parsimony tree.
getClans Clans, slices and clips
read.aa Read Amino Acid Sequences in a File
threshStateC Internal phangorn Functions
hadamard Hadamard Matrices and Fast Hadamard Multiplication
codonTest codonTest
read.nexus.splits Function to import and export splits and networks
phyDat Conversion among Sequence Formats
phangorn-package Phylogenetic analysis in R
splitsNetwork Phylogenetic Network
discrete.gamma Discrete Gamma function
distanceHadamard Distance Hadamard
NJ Neighbor-Joining
dist.p Pairwise Polymorphism P-Distances from DNA Sequences
Laurasiatherian Laurasiatherian data (AWCMEE)
getRoot Tree manipulation
modelTest ModelTest
chloroplast Chloroplast alignment
superTree Super Tree methods
dist.hamming Pairwise Distances from Sequences
Ancestors tree utility function
cladePar Utility function to plot.phylo
densiTree Plots a densiTree.
lento Lento plot
delta.score Computes the \(\delta\) score
identify.networx Identify splits in a network
pmlMix Phylogenetic mixture model
reexports Objects exported from other packages
CI Consistency Index and Retention Index
consensusNet Computes a consensusNetwork from a list of trees Computes a networx object from a collection of splits.
simSeq Simulate sequences.
plot.networx plot phylogenetic networks
cophenetic.networx Pairwise Distances from a Phylogenetic Network
maxCladeCred Maximum clade credibility tree
pmlCluster Stochastic Partitioning
mast Maximum agreement subtree
lli Internal maximum likelihood functions.
writeDist Writing and reading distances in phylip and nexus format
yeast Yeast alignment (Rokas et al.)
treedist Distances between trees
pml.control Likelihood of a tree.
multiphyDat2pmlPart Partition model.
upgma UPGMA and WPGMA
ancestral.pml Ancestral character reconstruction.
add.tips Add tips to a tree
allTrees Compute all trees topologies.
SH.test Shimodaira-Hasegawa Test
SOWH.test Swofford-Olsen-Waddell-Hillis Test
createLabel Compare splits and add support values to an object
coalSpeciesTree Species Tree
bab Branch and bound for finding all most parsimonious trees
bootstrap.pml Bootstrap
as.networx Conversion among phylogenetic network 0bjects
No Results!

Vignettes of phangorn

Name
Ancestral.Rnw
IntertwiningTreesAndNetworks.Rmd
Networx.Rmd
Trees.RData
Trees.Rnw
cophylo.png
exdna.txt
movie.gif
phangorn-specials.Rnw
phangorn.bib
primates.dna
seqLogo.pdf
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Details

LinkingTo Rcpp
License GPL (>= 2)
VignetteBuilder utils, knitr
URL https://github.com/KlausVigo/phangorn
BugReports https://github.com/KlausVigo/phangorn/issues
Repository CRAN
Encoding UTF-8
RoxygenNote 6.1.1
NeedsCompilation yes
Packaged 2019-06-18 15:48:42 UTC; klaus
Date/Publication 2019-06-19 04:40:03 UTC

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