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Wednesday, June 29 • 11:24am - 11:42am
The phangorn package: estimating and comparing phylogenetic trees

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Methods of phylogenetic reconstruction are nowadays frequently used outside computational biology like in linguistics and in form of hierarchical clustering in many other disciplines. The R package phangorn allows to reconstruct phylogenies using Maximum Likelihood, Maximum Parsimony or distanced based methods. The package offers many functions to compare trees through visualization (splits networks, lento plot, densiTree) and to choose and compare statistical models (e.g. modelTest, SH-test, parametric bootstrap). phangorn is closely connected with other phylogenetic R packages ape or phytools in the field of phylogenetic (comparative) methods.

avatar for Susan Holmes

Susan Holmes

Professor, Statistics, Stanford
I like teaching nonparametric multivariate analyses to biologists. | Reproducible research is really important to me and I make all my work available online, mostly as Rmd files. I still like to code, use Github and shiny as well as Bioconductor. I am trying to finish a book for biologists that includes code and a lot of fancy visualizations of `uncertainty'.

avatar for Klaus Peter Schliep

Klaus Peter Schliep

Department of Biology, University of Massachusetts Boston

Wednesday June 29, 2016 11:24am - 11:42am
Lane & Lyons & Lodato 326 Galvez Street Stanford, CA 94305-6105

Attendees (24)