What tools were used to draw these phylogenetic trees?

Question

[ivan.antonov]

Tree #1 from https://www.ncbi.nlm.nih.gov/pubmed/26773003 :

Tree #2 from http://www.fisht1k.org/subproject/phylogeny :

I would like to group sequences on the tree and have a table/graphics on the side. Also, it would be great if at least some part of this task can be done programmatically. I was wondering what could be a good tool (or an R library, for example) to do that?

Thank you in advance,
Ivan

[ivan.antonov]

Thanks everyone for the help! I currently use the Figtree tool for simple visualization. I will give the ggtree a try -- it could be a good way to annotate a big tree programmatically.

Cheers, Ivan

[WouterDeCoster]

Hi Ivan,

No need to close a thread when the question is answered ;-)

Cheers, Wouter

[ivan.antonov]

Ah, Ok! Thank you -- I didn't realize that :)

Answer 1

[WouterDeCoster]

I'm not sure if it will fit your needs exactly, but you can do many many things using ggtree in R http://bioconductor.org/packages/release/bioc/html/ggtree.html

Answer 2

[Brice Sarver]

Unfortunately, the answer is almost certainly Adobe Illustrator. It looks like trees were exported post-visualization using Figtree and manipulated/colored/added to after the fact.

[Farbod]

Dear Brice, Hi. I have two questions from you

1- is there any guide, tutorial or even youtube about how to use FigTree, you can suggest?

2- Why you have used "Unfortunately" ?

~ Best

[Brice Sarver]

1. It's very straightforward; I don't think you really need one. You load in a Newick or Nexus tree and select options from menus on the side. You can export as a variety of formats, including vector graphics.
2. "Unfortunately" in the sense that there's not a catch-all tool that will do all of the things that vanya.antonov wanted. Requires the use of graphic design tools.

[Farbod]

Dear Brice hi and thank you for your help,

Does programs same as MEGA6 or Phylogeny can produce this "Newick or Nexus tree" ?

~ Take care

[Guangchuang Yu]

all can be done using ggtree.

Answer 3

[Asaf]

There's iTOL as well, with a lot of presentation options. http://itol.embl.de/

Answer 4

[Ron]

Try some of the tools mentioned in this post: What Is A Good Phylogenetic Tree Display Program For Large Data Sets?

Answer 5

[tonu.margus]

There is an ETE toolkit what is a Python framework for the analysis and visualization of trees. It contains multiple tools and pipelines. Homepage is here http://etetoolkit.org/