There is many programs to choose from. First you need to decide what method you want to use. Parsimony is the most common for morphological dataset, but you can use both Bayesian and ML methods as well.
I have only use parsimony for morphological datasets, and I like the program NONA used in combination with Winclada
Hi Ravi. You need to decide on the analysis you want to do first and then you may opt for the software. Also have you think of any multivariate analysis you may do with your data? For instance using Primer software? I guess you will go into genetics as well and compare your morphological and genetic data? If you have access to the UOM library - you may look for my Bsc thesis where I did a phylogeny comparison based on morphological & genetic data. Good luck!