I want thank you all persons who kindly sent their suggestions.
Here below a summary of the indications I have got. They are listed
anonymously.
If someone want receiving the email address for a given report,
please, write me at
fbarbanera@biologia.unipi.it
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1. I have used three different approaches to estimate ancestral area
reconstruction. One is S-Diva (statistical dispersal vicariance) of
Yu et al. (2010) (http://mnh.scu.edu.cn/S-diva/blog/index.html),
which I believe has been superseded by RASP. I used the online
version of S-DIVA and it was quite easy to run. You can check my
paper Morales-Hojas et al. (2011) Mol. Phyl. Evol. 60. This method
allows for phylogenetic uncertainty and can be run with trees from
the posterior trees from a MrBayes analysis, and it gives you the
probabilities for each ancestral area. The output gives you a tree
with the probabilities in each node.
I have also used Mesquite to estimate ancestral area with Likelihood.
Mesquite is easy to use once you get the hang of it, and the method
it uses gives you the probabilities of each state in the node of the
phylogeny.
And finally you have SIMMAP (http://www.simmap.com/). It estimates
the posterior probabilities of character states for each internal
node. It has the advantage that it uses a Bayesian approach and
allows for uncertainty (you can run it with your posterior trees from
MrBayes), but the output is not very user friendly. Nevertheless is
not difficult to run and it is quite robust.
2. A good program to do that is MESQUITE. The program can perform
this through ML o parsimony analysis.
I hope that this information is usefull for you
3. Not sure if you could call these friendly but we have used 3area
and Lagrange. Good luck,
4. http://code.google.com/p/lagrange/
5. One quick suggestion would be the software PhyloMapper: http://
www.evotutor.org/PhyloMapper/
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Filippo Barbanera
Researcher
Department of Biology
Protistology-Zoology Unit
Via A. Volta, 6
I - 56126 Pisa (PI)
Italy
Web site: www.biologia.unipi.it
Skype: barba_skype
room: + 39 050 2211386
lab. : + 39 050 2211343
fax: + 39 050 2211393
Filippo Barbanera