Is there any software (desktop or online) that allows you to create customizable visualizations of the most current phylogenetic relationships between taxons? Let's say that I would like to have the illustration of phylogenetic relationship within extant mammals and extant birds and I would like to include different detail, like at the level of orders or at the level of families, or detailed relationship in selected order only. Then maybe change the layout little bit and export it into word processing software or save as vector graphics for further editing. Is there something like that? Something easy that students can use for the assignments and theses, etc. I think it would be handy if this would be possible in Tree of Life but I was not able to find any feature like this there. Do you have any ideas? Thank you!
Hi Pavel,
TimeTree is good for getting a decent divergence times between taxa.
OpenTreeofLife is great for getting cladograms of specific taxa. See https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-of-Life-APIs. It is very easy to provide a list of species and output a tree. There are lots of other options and sources of tree. Check it out!
Adam
The onezoom site is nice. It does not do exaclty what you are asking for, but it is worth exploring anyway for ideas about tree representations.
http://www.onezoom.org/
Hi Pavel,
Have a look at the dendogram option and ape package in R.
https://rpubs.com/gaston/dendrograms
It's very useful to customize phylogenetic tree and the students can start to familiarize with the R environment. Hope this can help!
Cheers,
Ago
If you have an alignment of some description figtree is very customisable.
http://tree.bio.ed.ac.uk/software/figtree/
Hi,
I would recommend the ETE toolkit http://etetoolkit.org. It is great at visualizations and it comes with documentation and tutorials.
Cheers,
Eduardo
Dear all, it has been a while since I posed my question and I apologize for being late with my own response. However, I finally got to look at your valuable suggestions. With your help, I learned few new things and got perfect answer for my question and even beyond that question.
I would like to summarize a few points:
Livio suggested www.timetree.org and I was able to find there pretty nice dendrograms for some of the taxons and very nice poster of tree of life. However, I think it is not possible to adjust the dendrograms in any way. Still it is good for the purpose I originally asked for and I think students could use it to illustrate phylogeny of their group very nicely.
Brian, Agostino, David and Eduardo suggested different software that can be used to visualize the trees. ETE Toolkit looks very very powerful but I could not find Windows version (just MacOS and Linux). In future, I hope to use OneZoom as it is indeed customizable (allows uploading own trees and metadata) and very attractive for public presentations. Eventually, I used FigTree which is powerful and very easy to use. I also found Interactive Tree of Life http://itol.embl.de/ which looks also nice. However, I needed to get the tree in text format to upload in these programs first...
Adam suggested Open Tree of Life. I was not able to find how to export the nice dendrogram pictures directly at the site but I found it is powerful to get the data for other programs. It took me a while to learn how to work with API (eventually, I found a good instructions here: https://blog.opentreeoflife.org/2014/10/07/tree-for-all-hackathon-series-introduction/ and used DHC Chrome extension to run API orders) and now I am able to extract the current dendrogram even for the small set of species I am only interested in and which are scattered across all vertebrates and then make a nice dendrogram in FigTree. Great for visualization purposes!
Thank you all! Best, Pavel
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