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Old 03-16-2012, 10:59 AM   #1
renesh
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Default phylogenetic tree

Hi friends,

I want colour the particular branch and taxa in phylogenetic tree to represent it effectively. I tried in various packages such as phylip, mega4, ugene but i am unable to do it. When i am trying to colour in mega4 and ugene , it is coloring all branches and taxa. But i want to colour specific one. I am having newick file for my phylogeny.

Please suggest me the way for this problem.
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Old 03-16-2012, 11:56 AM   #2
LeightonP
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You might find FigTree useful: http://tree.bio.ed.ac.uk/software/figtree/
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Old 03-16-2012, 02:44 PM   #3
renesh
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thank for your reply. Can you suggest me any other tool. This software is good but it can not change the size and colour of the font of taxa.

Last edited by renesh; 03-16-2012 at 02:48 PM.
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Old 03-16-2012, 07:45 PM   #4
JamesH
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Copy the tree and paste it into illustrator, or some other vector graphics program, then you can edit it and make it look the way you want, just be sure to constrain the proportions if you re-size it!
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Old 03-16-2012, 10:16 PM   #5
saemi
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Figtree is a great tool, if you export the tree as a graphic in a .svg file and uncheck something about text being drawn as shapes, you can work on it in illustrator and probably inkscape. Dendroscope is also useful, more options and more complicated http://ab.inf.uni-tuebingen.de/software/dendroscope/.

But you can change fonts and stuff in figtree, just select 'Tip Labels' and change font/colors.
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Old 03-17-2012, 03:18 AM   #6
LeightonP
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Quote:
Originally Posted by renesh View Post
thank for your reply. Can you suggest me any other tool. This software is good but it can not change the size and colour of the font of taxa.
As Saemi points out you can, in fact, change both the size and colour of font used for leaf labels.
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Old 03-17-2012, 03:47 PM   #7
renesh
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Thanks

I used that options(Tip label) for colour and font. But, using that option i able to change only font, but not the colour. Therefore, i changed the colour of branches to represent particular cluster.
can you suggest me how to change the colour for the label name using figtree?
I tried that tip label option for colour, but i am unable to do it.
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Old 03-20-2012, 09:24 AM   #8
ssing
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I also think the 'ape' package in R is great for making attractive trees, though it does require knowing R.
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