[Bioperl-l] Random trees generation

Jason Stajich jason.stajich at gmail.com
Fri Aug 3 11:52:48 EDT 2012


The current Bioperl random tree factory is for use with the coalescent which I needed for my research -- it may or may not be suitable for your purposes.
The module documentation echoes a call for more contribution to the implementations. 

Rutger's Bio::Phylo can generates random trees you can try it out too.
http://search.cpan.org/~rvosa/Bio-Phylo-0.50/lib/Bio/Phylo/Generator.pm


It really depends on what model you are trying to do. There are many tree simulators out there that may suit your needs better.
http://evolution.genetics.washington.edu/phylip/software.html#Simulation

Jason
On Aug 2, 2012, at 8:54 PM, Alexey Morozov <alexeymorozov1991 at gmail.com> wrote:

> Is it true that for generating random trees with integer branch lenghts I
> have to write my own generator? Seems like Tree::RandomFactory is only able
> to produce one with very small real values (and even that not at all
> branches). Is there no other good module fo that around?
> 
> Alexey.
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Jason Stajich
jason at bioperl.org




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