Question: plot phylogenetic tree with Figtree
0
gravatar for zhang248
23 months ago by
zhang24830
HZAU, China
zhang24830 wrote:

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. enter image description here

figtree phylogenetic tree • 2.8k views
ADD COMMENTlink modified 23 months ago • written 23 months ago by zhang24830

Please be more specific, your image is not accessible.

ADD REPLYlink written 23 months ago by Michael Dondrup46k

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

ADD REPLYlink written 23 months ago by zhang24830

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.

ADD REPLYlink written 23 months ago by Joe14k

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

ADD REPLYlink written 23 months ago by zhang24830

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

ADD REPLYlink written 23 months ago by Joe14k

Thanks, I'll try these tools.

ADD REPLYlink written 23 months ago by zhang24830

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

ADD REPLYlink modified 23 months ago • written 23 months ago by natasha.sernova3.6k

Thanks, I'll see them.

ADD REPLYlink written 23 months ago by zhang24830

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

ADD REPLYlink written 23 months ago by Kevin Blighe51k

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

ADD REPLYlink written 23 months ago by zhang24830
1
gravatar for Kevin Blighe
23 months ago by
Kevin Blighe51k
Kevin Blighe51k wrote:

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:

dend
imageupload

dend2

ADD COMMENTlink written 23 months ago by Kevin Blighe51k
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