Currently i'm using Phylogeny.fr tool for my analysis, but i have doubt whether to follow the same.
MEGA is easy
But I read MEGA is not suggested for protein seq, it is good for DNA seq.
MEGA 5 is a good one and also for protein seq
phylip
Maybe sth from the software poduced by CIBIV Vienna will be useful:
http://www.cibiv.at/software/
you can try
1. MAFFT (http://mafft.cbrc.jp/alignment/server/)...
2.TCOFEE (http://tcoffee.crg.cat/apps/tcoffee/do:regular)
3. Phylip
4. Phylemon (http://phylemon.bioinfo.cipf.es/)
etc
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