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.
Readme
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 | |
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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 |
depends | ape (>= 5.0) , R (>= 3.2.0) |
suggests | Biostrings , knitr , rgl , rmarkdown , seqinr , testthat , vdiffr , xtable |
imports | fastmatch , graphics , grDevices , igraph (>= 1.0) , magrittr , Matrix , methods , parallel , quadprog , Rcpp (>= 0.12.0) , stats , utils |
Contributors | Alastair Potts, Michelle Kendall, Emmanuel Paradis, Leonardo de Oliveira Martins, Tim W. White, Cyrill Stachniss, Keren Halabi, Richel Bilderbeek, Kristin Winchell |
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