plot phylogenetic tree with Figtree

Question

[zhang248]

I'm using figtree to plot a phylogenetic tree, can anyone tell me how to plot the out circle or a manual for Figtree? The circle with green,blue and yellow colours.

[Michael]

Please be more specific, your image is not accessible.

[zhang248]

I'm soory, my network was broken last night. And I have upload the image.

[Joe]

You want a circular tree? Then ensure you use the "Radial" type tree (I think it's the middle button under the "Layout" tab on the left hand side. The software is pretty straightforward though. The manual will be online at the figtree website, and/or in the archive you download when obtaining the software I should think.

[zhang248]

Thanks for your reply. I just want to draw the circle outside of the tree.

[Joe]

To my knowledge, figtree doesn't have that ability/feature. You may want to consider other tools such as Dendroscope or Anvio

[zhang248]

Thanks, I'll try these tools.

[natasha.sernova]

There is no manual here, only README.txt file.

Figtree turned out to be a nice program, thank you.

http://www.jcsantosresearch.org/Class_2014_Spring_Comparative/pdf/week_6/Feb_12_2015_Chronograms.pdf

Two other help versions:

http://tree.bio.ed.ac.uk/software/figtree/

See circular examples in the middle. See the post above as well.

And this one: http://w3.ualg.pt/~rcastil/SOFTWARE_WINDOWS/FigTree%20v1.2.3/README.txt

[zhang248]

Thanks, I'll see them.

[Kevin Blighe]

For a very rapidly-produced circular dendrogram / 'phylogenetic tree', see my posting here: A: how to draw circular dendrogram with distance information

[zhang248]

Thanks, Kevin. But it's diffcult to manipulate the tree for me.

Answer 1

[Kevin Blighe]

It was built using the dendextend package in R. There are many more things that you can do with this package including (I believe) everything that you need to do. Take a look at the tutorial Introduction to dendextend

It utilises also the Circos functions:

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