ape

MaRDI QIDQ16740swMATHCRANFDO

Authors Gilles Didier, Daniel J. Lawson, Santiago Claramunt, Olivier Gascuel, Guillaume Louvel, Joseph W Brown, Johan Nylander, Hoa Sien Cuong, Klaus Schliep, Bradley R. Jones, Jim Lemon, Emmanuel Paradis, Manuela Royer-carenzi, Thomas Guillerme, Simon P Blomberg, Julien Claude, Ben Bolker, Rainer Opgen-rhein, Benoit Durand, Christoph Heibl, Rj Ewing, Eric Marcon, Franz Krah, Rosemary Mccloskey, Julien Y Dutheil, Anthony R. Ives, Vincent Lefort, Andrei-alin Popescu, Richard Desper, Pierre Legendre, Korbinian Strimmer, Damien de Vienne

Last update 13 March 2023

Copyright license GNU General Public License, version 3.0, GNU General Public License, version 2.0

Software version identifier 5.7-1

Official website https://cran.r-project.org/package=ape

Source code repository https://github.com/cran/ape

Cited in

(only showing first 100 items - show all)

• An introduction to clustering with R
• Identifying anticancer peptides by using a generalized chaos game representation
• The impact of genetic diversity statistics on model selection between coalescents
• Gaussian approximations for phylogenetic branch length statistics under stochastic models of biodiversity
• New Gromov-inspired metrics on phylogenetic tree space
• Modeling rate of adaptive trait evolution using Cox-Ingersoll-Ross process: an approximate Bayesian computation approach
• Testing for correlation between traits under directional evolution
• Statistical analysis of network data with R
• Identical inferences about correlated evolution arise from ancestral state reconstruction and independent contrasts
• Exact and approximate limit behaviour of the Yule tree's cophenetic index
• Book review of: R. Gentleman et al., Bioinformatics and computational biology solutions using R and bioconductor
• Tropical sufficient statistics for persistent homology
• On statistical tests of phylogenetic tree imbalance: The Sackin and other indices revisited
• Tropical Fermat-Weber points
• Modern data science with R
• A generalized framework for analyzing taxonomic, phylogenetic, and functional community structure based on presence-absence data
• Reduced multidimensional scaling
• Impacts of phylogenetic dilution and concentration effects on species diversity and distribution patterns
• Random phylogenies and the distribution of branching times
• A comparison of ancestral state reconstruction methods for quantitative characters
• Sequential importance sampling for multiresolution Kingman-Tajima coalescent counting
• Functional and phylogenetic ecology in R
• compositions
• SCHUR
• ade4
• CanoDraw
• cocorresp
• cluster (R)
• FD
• gclus
• labdsv
• numecolR
• mvpart
• MVPARTwrap
• ROCR
• sedaR
• ArcView
• vegan
• MCF
• adegenet
• sna
• PHENIX
• geometry
• network
• networkDynamic
• pixmap
• tergm
• prabclus
• MrBayes
• PHYLIP
• RAxML
• clustvarsel
• PAUP*
• adephylo
• BIONJ
• GOSim
• Clustal
• GeoDa
• BEAST
• MorphoJ
• LASER
• MAFFT
• MCMCglmm
• MODELTEST
• pegas
• Picante
• phangorn
• SeqinR
• Seq-Gen
• Pysal
• MEGA
• Spectronet
• Mesquite
• bipartite
• GUniFrac
• phytools
• phylobase
• Rsundials
• SDMTools
• HMMER
• PAML
• PhyML
• GOstats
• Momocs
• EMP
• mixer
• BEAGLE
• BEAUti
• pIQPNNI
• SplitsTree
• Phyloseq
• homals
• shapes
• rimage
• rwty
• FASTA3
• cobalt
• etl
• EpiModel
• shazam

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