Question: What tools were used to draw these phylogenetic trees?
1
gravatar for ivan.antonov
2.6 years ago by
ivan.antonov70
Moscow, Russia
ivan.antonov70 wrote:

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

enter image description here

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

enter image description here

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

ADD COMMENTlink modified 2.6 years ago by Asaf5.6k • written 2.6 years ago by ivan.antonov70

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

ADD REPLYlink written 2.6 years ago by ivan.antonov70

Hi Ivan,

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

Cheers, Wouter

ADD REPLYlink written 2.6 years ago by WouterDeCoster39k

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

ADD REPLYlink written 2.6 years ago by ivan.antonov70
7
gravatar for WouterDeCoster
2.6 years ago by
Belgium
WouterDeCoster39k wrote:

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

ADD COMMENTlink written 2.6 years ago by WouterDeCoster39k
3
gravatar for Brice Sarver
2.6 years ago by
Brice Sarver2.6k
United States
Brice Sarver2.6k wrote:

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.

ADD COMMENTlink written 2.6 years ago by Brice Sarver2.6k

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

ADD REPLYlink written 2.6 years ago by Farbod3.2k
1
  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.
ADD REPLYlink written 2.6 years ago by Brice Sarver2.6k

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

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Farbod3.2k

all can be done using ggtree.

ADD REPLYlink written 2.6 years ago by Guangchuang Yu2.1k
1
gravatar for Asaf
2.6 years ago by
Asaf5.6k
Israel
Asaf5.6k wrote:

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

ADD COMMENTlink written 2.6 years ago by Asaf5.6k
0
gravatar for Ron
2.6 years ago by
Ron930
United States
Ron930 wrote:

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

ADD COMMENTlink written 2.6 years ago by Ron930
0
gravatar for tonu.margus
2.6 years ago by
tonu.margus20
Sweden, Umeå, Umeå University
tonu.margus20 wrote:

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/

ADD COMMENTlink written 2.6 years ago by tonu.margus20
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