CRAN/E | phangorn

phangorn

Phylogenetic Reconstruction and Analysis

Installation

About

Allows for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation (Schliep 2011). Offers methods for tree comparison, model selection and visualization of phylogenetic networks as described in Schliep et al. (2017).

Citation phangorn citation info
github.com/KlausVigo/phangorn
klausvigo.github.io/phangorn/
Bug report File report

Key Metrics

Version 2.11.1
R ≥ 4.1.0
Published 2023-01-23 457 days ago
Needs compilation? yes
License GPL-2
License GPL-3
CRAN checks phangorn results
Language en-US

Downloads

Yesterday 477 -16%
Last 7 days 3.014 -17%
Last 30 days 13.023 -15%
Last 90 days 43.646 +11%
Last 365 days 169.047 -11%

Maintainer

Maintainer

Klaus Schliep

klaus.schliep@gmail.com

Authors

Klaus Schliep

aut / cre

Emmanuel Paradis

aut

Leonardo de Oliveira Martins

aut

Alastair Potts

aut

Iris Bardel-Kahr

aut

Tim W. White

ctb

Cyrill Stachniss

ctb

Michelle Kendall

ctb

Keren Halabi

ctb

Richel Bilderbeek

ctb

Kristin Winchell

ctb

Liam Revell

ctb

Mike Gilchrist

ctb

Jeremy Beaulieu

ctb

Brian O'Meara

ctb

Long Qu

ctb

Joseph Brown

ctb

Santiago Claramunt

ctb

Material

README
NEWS
Reference manual
Package source

In Views

Phylogenetics

Vignettes

Markov models and transition rate matrices
Ancestral Sequence Reconstruction
Intertwining phylogenetic trees and networks: R Example Script
Maximum likelihood by hand
Phylogenetic trees from morphological data
Splits and Networx
Estimating phylogenetic trees with phangorn

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

phangorn archive

Depends

ape ≥ 5.6
R ≥ 4.1.0

Imports

digest
fastmatch
generics
graphics
grDevices
igraph ≥1.0
Matrix
methods
parallel
quadprog
Rcpp
stats
utils

Suggests

Biostrings
knitr
magick
rgl
rmarkdown
seqinr
seqLogo
tinytest
xtable

LinkingTo

Rcpp

Reverse Depends

apex
MonoPhy
MSCquartets
sangeranalyseR
windex

Reverse Imports

babette
beastier
BoSSA
BSS
coalescentMCMC
corHMM
datelife
DCLEAR
DIAlignR
dispRity
dowser
EnvNJ
genBaRcode
haplotypes
hisse
immunarch
indelmiss
ips
liayson
LymphoSeq
markophylo
MesKit
microbial
nodeSub
OUwie
paleotree
pcmabc
philr
phyloregion
phytools
pirouette
POMS
prewas
rapidphylo
recluster
rwty
scistreer
SeqFeatR
sketching
STraTUS
tanggle
taxize
TreeDist
treespace

Reverse Suggests

ape
compcodeR
CongreveLamsdell2016
gromovlab
mcbette
MicrobiotaProcess
msa
pagoo
Platypus
Quartet
RevGadgets
RRphylo
shipunov
tracerer
treeio
TreeSearch
TreeTools

Reverse Enhances

dendextend