Question: Software for Tree Visualization
1
gravatar for l.souza
11 months ago by
l.souza60
Brasilia, Brazil
l.souza60 wrote:

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

ADD COMMENTlink modified 11 months ago by Biojl1.6k • written 11 months ago by l.souza60

there is a ggtree package you can take a look.

ADD REPLYlink written 11 months ago by Ming Tang2.3k

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

ADD REPLYlink written 11 months ago by l.souza60
1

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

ADD REPLYlink written 11 months ago by Ming Tang2.3k
6
gravatar for cfos4698
11 months ago by
cfos469890
cfos469890 wrote:

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.

ADD COMMENTlink written 11 months ago by cfos469890
4
gravatar for Biojl
11 months ago by
Biojl1.6k
Barcelona
Biojl1.6k wrote:

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.

ADD COMMENTlink modified 11 months ago • written 11 months ago by Biojl1.6k
2

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

ADD REPLYlink written 11 months ago by jrj.healey3.9k
2
gravatar for jrj.healey
11 months ago by
jrj.healey3.9k
United Kingdom
jrj.healey3.9k wrote:

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

ADD COMMENTlink modified 11 months ago • written 11 months ago by jrj.healey3.9k
1
gravatar for lh3
11 months ago by
lh330k
United States
lh330k wrote:

See my old answer here.

ADD COMMENTlink written 11 months ago by lh330k
1

No other software since 6.3 years?

ADD REPLYlink written 11 months ago by Rob90
1
gravatar for Lila M
11 months ago by
Lila M 370
UK
Lila M 370 wrote:

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

ADD COMMENTlink written 11 months ago by Lila M 370
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