I need to produce a large number of coalescent trees for simulations. My code is in R and rtreeshape seems quite good but in a paper I am using as reference evolver of the PALM package was used. Does the software used makes a big difference in the randomization results?
As far as I can tell, rtreeshape and PAML's evolver do NOT generate trees under the coalescent model. I couldn't find what model uses PAML, but if you can find out and is one of the models used by rtreeshape (Yule, PDA, Biased models) it shouldn't be a difference, should it?
If you need to use the coalescent model (intra-species genealogy), you probably need some different software. There are several coalescent simulation programs available which will do pretty much the same for the "standard coalescent" but that will have different features that could be required for specific problems (different mutational models, different demographic scenarios, recombination...). Some examples:
Hudson ms: http://home.uchicago.edu/rhudson1/source/mksamples.html
FastSimCoal : http://cmpg.unibe.ch/software/fastsimcoal/
netrecodon: http://code.google.com/p/netrecodon/
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