Constructing Rooted Trees
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12.2 years ago
figo ▴ 220

Hi all,

I used phyml to make ML trees which are unrooted in newick format but all the trees contains an outgroup. Now i want to make all trees rooted using that outgroup .I tried to look for softwares like phylip ,emboss has module in that but i have a large number of trees.

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There is loads of software to make rooted trees, can you be more specific what your goal is and what kind of trees you have? Is there already an outgroup in the trees, or will you be adding an outgroup? what software did you use to make the 500 unrooted trees and in what format do you have them now?

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i used phyml to make ML trees which are unrooted in newick format but all the trees contains an outgroup. Now i want to make all trees rooted using that outgroup .I tried to look for softwares like phylip ,emboss has module in that but i have a large number of trees.

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update your question with this information please

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12.2 years ago

You can do this with njplot, just have to open your Newick formatted tree (classical output format, also used by phyml). Than, just click 'New Outgroup' and choose the one you want and save it.

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12.2 years ago
jhc ★ 3.0k

Hi Figo,

Assuming the simplest scenario, you would just need a script that opens each tree, looks for the outgroup sequences and use them to root the tree. Here is how I would do it using the

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