I suggest TNT: http://www.lillo.org.ar/phylogeny/tnt/

For a comprehensive list of phylogeny programs, check out Joe Felsenstein's page:

http://evolution.genetics.washington.edu/phylip/software.html

http://www.lillo.org.ar/phylogeny/tnt/

http://evolution.genetics.washington.edu/phylip/software.html

Hello Surajit,

As Yuri mentioned you can use TNT for a parsimony approach or you can use MrBayes for a Bayesian approach. These are probably the easiest and most robust methods.

Best Regards 

You should apply  analysed under maximum parsimony, followed by successive reweighting and implied weighting as optimality criteria. Tree searches by using a Wagner tree as the starting tree plus tree bisection and reconnection (TBR), with ten trees saved per replication and also by TBR branch swapping. Analyses with implied weighting were conducted in TNT 1.1

(Goloboff, Farris & Nixon, 2008)  Goloboff

et al. (2008).  you should used maximum parsimony with successive reweighting by PAUP 4.0b10 (Swofford, 2002). Character supports calculation with TNT. 

Try Using Mesquite. Wonderful versatile software

I suggest Mesquite to create a character matrix and use TNT or PAUP for the parsimony approaches.

http://mesquiteproject.org/mesquiteArchives/mesquite2.75/mesquite/download/installationWindows.html

http://www.lillo.org.ar/phylogeny/tnt/

Good luck

Actually now you can combine PAUP or TNT to the mesquite itself using a package called Zephyr and it makes the whole parsimony approach much more easy.