Thank you for your guidance.

Both softwares are well documented. If you don't have much experience with the command-line and would like to get up-and-running quickly, you might want to check out the Cipres portal which will allow you to run both by filling in options via a graphical web page: https://www.phylo.org. This used to be free but I'm not sure if this is still the case. Good luck!

Also check out http://iqtree.cibiv.univie.ac.at

Thank you very much

Finally I wrote this command line for MrBayse on linux terminal:

mb

exe [input file address-nexuse format]

prset aamodelpr=fixed(jones);

lset rates=invgamma ngammacat=4;

mcmcp ngen=100000000 relburnin=yes burninfrac=0.25 printfreq=1000 samplefreq=1000 nchains=4 temp=0.15 savebrlens=yes stoprule=yes stopval=0.015;

mcmc;

sumt;

sump;