Hy Mohd,
There was recently a nice review about all the alignment software available. You might find one you like in there.
Visualization of multiple alignments, phylogenies and gene family evolution.
http://www.nature.com/nmeth/journal/v7/n3s/abs/nmeth.1434.html
By the way there's also a review on structures visualization software in the same supplement issue about visualizing biological data, that might interest other readers form that list as well.
Visualization of macromolecular structures.
http://www.nature.com/nmeth/journal/v7/n3s/abs/nmeth.1427.html
Best,
Luc
--
Luc Bonnefond, PhD.
Division of Structure Biology
Department of Basic Medical Sciences,
Institute of Medical Science,
The University of Tokyo
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