Alignment queires

[Tarak Parekh]

Hello,
I am a novice at performing alignment of amino acids.
I need to know some basics of protein alignment. Currently
I am using GCG to perform protein alignment. I would like to 
how does Clustal help in alignment ? 
Is likelihood method different from alignment performed by GCG.
I have some more queries too. I am slightly confused(probably more)
about these things.
Please email me, if you can spare some time to answer some basic
queries.

thanks, 
tarak
Email : tarak at cs.arizona.edu