Analysis of phylogenetics and evolution with R

DOI10.1007/978-1-4614-1743-9MaRDI QIDQ3225374zbMATH OpenOpenAlexFDO

Authors Emmanuel Paradis

Publication date 19 March 2012

Full work available at URL https://doi.org/10.1007/978-1-4614-1743-9

Mathematics Subject Classification ID

Applications of branching processes (60J85) Applications of statistics to biology and medical sciences; meta analysis (62P10) Research exposition (monographs, survey articles) pertaining to biology (92-02) Software, source code, etc. for problems pertaining to biology (92-04) Problems related to evolution (92D15)

Recommendations

• Analysis of Phylogenetics and Evolution with R
• Reconstructing the phylogeny: computational methods
• Functional and phylogenetic ecology in R
• Morphometrics with R
• Getting started with R. An introduction for biologists.

Cited in

(8)

• Putting phylogeny into the analysis of biological traits: a methodological approach
• Phylogenetically informed Bayesian truncated copula graphical models for microbial association networks
• Bayesian evolutionary analysis with BEAST
• Phylogenetic effective sample size
• Analysis of Phylogenetics and Evolution with R
• Functional and phylogenetic ecology in R
• Hit and Run Sampling from Tropically Convex Sets
• Parameter estimation for fractional birth and fractional death processes

Describes a project that uses

Uses Software

• Seq-Gen
• phangorn
• Clustal
• PHYLIP
• MrBayes
• R
• ape
• adegenet
• pegas
• MODELTEST
• LASER
• SeqinR
• BIONJ
• MCMCglmm
• adephylo
• MAFFT
• Picante

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