generating random newick tree

Question

[Quak]

What are some smart ways of generating newick tree string randomly, say, with 128 leaf for example ...

Answer 1

[Brice Sarver]

There are several ways to do this in R.

rtree() in the ape library will simulate a random tree.

The TreeSim library will allow you to simulate trees under various parameter combinations and constrain on the number of taxa, age, etc. I use it for simulations and when I need a quick dummy tree.

Save the objects in Newick format once you've got what you want.

[Quak]

thanks; The thing is I would like the tree to be equidistant !! I should have said that earlier in the question, It would be nice to know how can I constrain the simulation to make equidistance tree ...

[Brice Sarver]

Just to be clear, by 'equidistant' do you mean 'ultrametric'? TreeSim will produce ultrametric trees.

[Quak]

sorry about the confusion; I have pasted an image under the other answer ... I hope that makes it clear :-)

Answer 2

[Pierre Lindenbaum]

A quick solution in C?

[Quak]

Great; I am trying to tweak it; basically, I would like to have a equidistance tree ... something like this, with 128 or more leafs ...

[Pierre Lindenbaum]

Easy if you only specify the number of terminal nodes. Is it what you want?

[Quak]

Exactly;

Given 7 number of nodes, ./a.out 7 It returns

(((id5:1.000000)id3:1.000000)id0:1.000000,(id2:1.000000)id1:1.000000,id4:1.000000)id6;

which does not look as I expect either.

[Pierre Lindenbaum]

In your example, there are 3 terminal nodes, not 7.

[Quak]

Yes, 7 is the total number of nodes; meaning 4 leafs, 2 parents and 1(origin).