Hey, I want to get a Conservation Plot across 4 - 5 species. I researched Multiple Sequence Alignment viewers and I encounterd eShadow, zPicture and SeqTools (Belvu). I got different results from eShadow and zPicture (or I have difficulties putting together the results). I am preparing to install SeqTools now. However, for Belvu, I need to prepare the aligned-FastQ file (I am going to use ClustalW) and then upload it in Belvu (as far as I read).
What do you think? Is this the right approach for obtaining a Conservation Plot? Do you have any opinions or preferences on MSA viewers?