Question: Constructing Rooted Trees
3
gravatar for figo
8.4 years ago by
figo200
figo200 wrote:

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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ADD COMMENTlink modified 7.1 years ago by Biostar ♦♦ 20 • written 8.4 years ago by figo200
1

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?

ADD REPLYlink written 8.4 years ago by Niek De Klein2.5k

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.

ADD REPLYlink written 8.4 years ago by figo200

update your question with this information please

ADD REPLYlink written 8.4 years ago by Niek De Klein2.5k
2
gravatar for Leonor Palmeira
8.4 years ago by
Leonor Palmeira3.7k
Liège, Belgium
Leonor Palmeira3.7k wrote:

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.

ADD COMMENTlink written 8.4 years ago by Leonor Palmeira3.7k
1
gravatar for jhc
8.4 years ago by
jhc2.9k
Spain
jhc2.9k wrote:

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

ADD COMMENTlink written 8.4 years ago by jhc2.9k
1

Something is missing from this answer?

ADD REPLYlink modified 4.7 years ago • written 4.7 years ago by rezam20
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