I think the Mega 6 (http://www.megasoftware.net/) is good for that  ,

I think you should use several programs for that. Especially BEAST, PAUP etc... You should interpret that results and do your work.

U can also use GENEIOUS  

http://www.geneious.com/

But MEGA is more available 

PAUP certainly present no problems i doing this. 

Hi Hugo,

Another good program to concatenate genes into a super matrix is FASconCat. See here:

http://zfmk.de/web/Forschung/Abteilungen/AG_Wgele/Software/FASconCAT/index.en.html

There is a good manual and the program can give output in various formats including nexus, phylip and fasta. It also gives some basic info on the composition of the super matrix and proportion of missing data etc.

Thank you guys!

I had been used "SuperMatrix 1.7.8", but the output data not run in the MrBayes.

I will test these program that you suggested for me and give feedback.

Best wishes for all!