Question: What Phylogeny Viewing Software Do You Use?
11
gravatar for Roderic Page
9.4 years ago by
Roderic Page390
Glasgow
Roderic Page390 wrote:

There are numerous phylogeny viewing programs available, which ones do people use most often? Are there features (e.g., visualisations, data formats, size of tree that can be displayed, annotation) that people feel existing software lack?

I'll declare an interest. I'm the author of http://taxonomy.zoology.gla.ac.uk/rod/treeview.html, which is beginning to show its age. There are some other great tools around, so I'm trying to gauge whether TreeView should be allowed to die gracefully, of whether I should invest time in developing it further (see http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/ ).

ADD COMMENTlink modified 8.4 years ago by Dataminer2.6k • written 9.4 years ago by Roderic Page390
2

Any answer is subjective. I don't agree with this retagging.

ADD REPLYlink written 9.3 years ago by Paulo Nuin3.7k
2

I removed the "subjective" tag.

ADD REPLYlink written 9.3 years ago by Paulo Nuin3.7k

It's not an answer to Rod's question, but just want to highlight Joe Felsenstein's list of phylogeny-related software here:

http://evolution.genetics.washington.edu/phylip/software.html

It's a great place to go if you're looking for possible software/tools in this field.

Here's the link to the list of tree visulalisation software: http://evolution.genetics.washington.edu/phylip/software.html#Interactive

ADD REPLYlink written 6.6 years ago by aidan-budd1.9k
7
gravatar for Jarretinha
9.4 years ago by
Jarretinha3.3k
São Paulo, Brazil
Jarretinha3.3k wrote:

I normally use FigTree for a quick and flexible look on phylogenetic data. For small datasets, PHYLIP DRAWTREE or TreeView are enough. But, for printing I really look for some adequate LaTeX package, commonly PSTricks. It's cumbersome but it works and is beautifull, fully customizable. For large trees, some scripting is necessary. But, now there is E.T.E. which is quite handy.

I'm happy to see Rod Page in this forum. Your books on phylogenetics and molecular evolution are part of my everyday life. I do appreciate the effort !!!

ADD COMMENTlink written 9.4 years ago by Jarretinha3.3k

Me too. I'm reading this book on the bus each morning.

ADD REPLYlink written 9.4 years ago by Michael Barton1.8k

You might also take a look at Gram http://www.bmnh.org/~pf/gram.html - a Python module on top of Latex TikZ for tree drawing

ADD REPLYlink written 9.3 years ago by Cymon0

That'll be http://www.bmnh.org/web_users/pf/gram.html then...

ADD REPLYlink written 9.0 years ago by Cymon0
5
gravatar for Phis
9.4 years ago by
Phis1.0k
CH
Phis1.0k wrote:

I usually do use TreeView. While it may not be particularly new, I think it's stood the test of time well. I've also used Mesquite and some other tools, but I always find myself coming back to TreeView per default.

Among my colleagues, many also use TreeView, so I am sure that if you did put in the effort to update/enhance TreeView, there'd be many who would greatly appreciate it.

Last, but not least: THANK YOU for having produced this gem!

ADD COMMENTlink modified 9.4 years ago • written 9.4 years ago by Phis1.0k
5
gravatar for Khader Shameer
9.4 years ago by
Manhattan, NY
Khader Shameer18k wrote:

Tried Phyfi]1 for quick trees or iTOL whenever I need that super cool phylogeny tree figure for a publication. I have used TreeView and MEGA earlier. Tried couple of programs from the list of The Phylogeny Tree Drawing / Plotting program from Phylip page.

ADD COMMENTlink modified 9.4 years ago • written 9.4 years ago by Khader Shameer18k
4
gravatar for Rutger Vos
9.4 years ago by
Rutger Vos40
Netherlands
Rutger Vos40 wrote:

I really have one main usage for TreeViewX, and that is to quickly visualize a tree from the clipboard when I'm coding. I used TreeView for that previously, but I think I can't run that any more on my new OSX version (10.7 Pussycat or whatever). I vaguely miss the ability to show unrooted trees, which TreeView used to have but the X version doesn't seem to. All in all I find either very handy for this one use case. Other programs (e.g. mesquite) just aren't lightweight and quick enough.

ADD COMMENTlink written 9.4 years ago by Rutger Vos40
4
gravatar for Abhiman
9.3 years ago by
Abhiman130
Hyderabad, INDIA
Abhiman130 wrote:

To make a phylogenetic tree one needs a software which makes the tree initially, so I use mega,phylip,molphy to make the initial tree. For making annotations and publication quality trees, I use TreeDyn [ http://www.treedyn.org/ ]. For quick visualisation of trees I use these online tools

ADD COMMENTlink modified 9.3 years ago • written 9.3 years ago by Abhiman130
3
gravatar for Michael Barton
9.4 years ago by
Michael Barton1.8k
Akron, Ohio, United States
Michael Barton1.8k wrote:

I like FigTree because it allows me to play with the tree a little bit to mark-up the regions I'm interested in, unfortunately it's Mac OSX only though. Scriptree also seems quite good.

With the availability of larger sequencing data sets I'd like to see tree viewers be able to help distill a phylogenetic tree down to the points of interest. I'd like to be able to use colours and branch grouping to highlight to the reader what I think is relevent.

ADD COMMENTlink written 9.4 years ago by Michael Barton1.8k
2

FigTree is a cross platform Java program (the screen shot shows it running on Mac OS X, but it runs on Windows and Unix/Linux as well).

ADD REPLYlink written 9.4 years ago by Roderic Page390

Ok. I think I got the impression because it looks so native to Aqua.

ADD REPLYlink written 9.4 years ago by Michael Barton1.8k
2
gravatar for Giovanni M Dall'Olio
9.4 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

I am not too much into this, but I have used: jalview, seaview, mega (on linux throught wine).

All of these are not specifically developed for visualizing trees, however they have the ability to do so and for my needs it is enough.

ADD COMMENTlink written 9.4 years ago by Giovanni M Dall'Olio26k
2
gravatar for Paulo Nuin
9.3 years ago by
Paulo Nuin3.7k
Canada
Paulo Nuin3.7k wrote:

I haven't seen Dendroscope mentioned in the answers. Very good application too.

ADD COMMENTlink written 9.3 years ago by Paulo Nuin3.7k
0
gravatar for Adam
8.4 years ago by
Adam10
Adam10 wrote:

I've had a lot of luck with PFAAT, available @ pfaat.sourceforge.net. Not only can you view/create trees, but you can edit the multiple sequence alignments used to generate them.

very useful!

ADD COMMENTlink written 8.4 years ago by Adam10
0
gravatar for Dataminer
8.4 years ago by
Dataminer2.6k
Netherlands
Dataminer2.6k wrote:

PHYLIP, TreeView, MEGA and the list goes on ..... it depends upon how big your dataset is as stated by Jarretinha.

ADD COMMENTlink written 8.4 years ago by Dataminer2.6k
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