Software for Tree Visualization

Question

[l.souza]

What is the best bioinformatic software for visualization of trees generated by RAxML?

[Ming Tommy Tang]

there is a ggtree package you can take a look.

[l.souza]

This is R, right? I'm gonna take a look!

[Ming Tommy Tang]

yes https://github.com/GuangchuangYu/ggtree check if it takes your format as input or not.

Answer 1

[cfos4698]

There are a variety of packages within R that can be used to plot phylogenetic trees, such as ggtree (as pointed out by tangming2005). These are useful if you want to script the plotting of your trees. However, the packages can be pretty tricky to work with/optimize to get nice-looking, legible trees as an output.

Instead, I've pretty much always stuck to using FigTree (http://tree.bio.ed.ac.uk/software/figtree/) since it does everything I need and is easy to use. The trees look fairly basic, but can be tidied up elsewhere. If you choose to also visualize the trees from Bayesian analyses, I'd recommend checking out DensiTree (https://www.cs.auckland.ac.nz/~remco/DensiTree/). It can plot the sets of trees in the posterior distribution in some pretty neat ways.

[nsmi8446]

I still come back to this response. Thank you!

Answer 2

[Biojl]

My favourite is ETE3. You can draw beautiful trees, personalize them to an unprecedented level but most importantly, it allows you to programatically work with trees, asking all sort of questions and even storing information you generate within the trees.

A true jewel for researchers working with phylogenetic trees.

[Joe]

ETE3 is my absolute favourite commandline tool. the --text tree view is so neat to quickly glance at a tree without having to open an Xterm window

Answer 3

[lh3]

See my old answer here.

[Rob]

No other software since 6.3 years?

Answer 4

[Joe]

As mentioned:

• ggtree
• FigTree (my favorite)
• njplot
• ETE3
• Dendroscope

The list goes on...

Also if you just google your post title pretty much, you'll get this:

https://en.wikipedia.org/wiki/List_of_phylogenetic_tree_visualization_software

Answer 5

[Lila M]

As previously mentioned, there are lot of good programs. FigTree is also my favorite (http://beast.bio.ed.ac.uk/figtree). I recommended you to have a look in this web site, you will find something that will cover your needs! http://evolution.genetics.washington.edu/phylip/software.html