Illustration tools for phylogeny

[DrAshleyField]

G'day all,

I am interested in some ideas and discussions around illustration tools for phylogeny. Specifically, for the preparation of figures for publication where you may want to add images or annotate the tree with more than the basics. There are several out there, e.g. Dendroscope, Evolview, FigTree, ggtree, iTOL, Phylolink, What do you recommend? And why?

Thank you, Ashley Field

[joelnitta]

AFAIK dendroscope is no longer supported. When I try to go to the download page I get a 404, has been that way for at least one year now.

FigTree is fine if you have a basic tree and only need to show support values, also good if you don't want to do any coding. Probably not good for more advanced plotting of traits on the tree.

iTOL I think is better for plotting traits on the tree, especially if you don't have advanced R skills.

If you have moderate to advanced R skills and want to have a figure that can be reproduced using code, I recommend the following R packages: ggtree, ape, and phytools. ggtree is better if you are more used to ggplot2 syntax, ape is better if you are used to base R plot syntax, and phytools is better if you have the results of a phytools analysis / are used to base R syntax.

Finally, one tool you may have missed: taxonium, an online tree viewer. I love this tool for big trees, it is a great replacement for dendroscope in that respect. This is what I use for FTOL. The trait plotting is a bit limited though.

[DrAshleyField]

Thanks Joel. Much appreciated, as always.