Graphics

Inkscape is a vector graphic editor. It works with SVG files, but can also import PDF files. It is a great companion to R, which can export any graph in SVG:

hist(rnorm(1000), col="orange")
dev.print(svg, file="export.svg", width=12, height=8)

Gimp is an extremely complete image editor. It can also import from PDF at any resolution and export at almost any possible picture format.

Statistics

Well, of course, the R project is unavoidable, and its young companion Rstudio. Some very useful packages include

• ape, for tree and sequence manipulations, plotting, and all kind of comparative analysis
• phangorn, providing more specialized tools for tree manipulation such as midpoint rooting
• seqinr, providing access to ACNUC and all sequence databases, sequence manipulation tools and codon usage analysis
• RColorBrewer, bring the famous Brewer palettes to R
• agricolae, provides tools for posthoc analyses such as Tukey’s test, also for non-parametric tests such as Kruskal-Wallis