A workflow with R: Phylogenetic analyses and visualizations using mitochondrial cytochrome b gene sequences

Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data

(2019) Li-Gen Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R

(2012) Andrei-Alin Popescu et al.   BIOINFORMATICS

Bios2mds: an R package for comparing orthologous protein families by metric multidimensional scaling

(2012) Julien Pelé et al.   BMC BIOINFORMATICS

pegas: an R package for population genetics with an integrated-modular approach

(2010) E. Paradis   BIOINFORMATICS

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS