The basic information from a multiple alignment of protein sequences is the position and nature of the conserved regions in each member of the group. Conserved sequence regions correspond to functionally and structurally important parts of the protein. Multiple alignments let us transfer that knowledge to the other members in the group. Hypotheses about functional importance or specific roles can then be directly tested by mutagenesis and truncation experiments. Viewing Multiple alignments of many sequences and those with different sequence weights are difficult to visualize.
Sequence logos are a graphical way for presenting multiple alignments.
The logo shows the aa present in each alignment position. The higher the aa and the stack the more conserved they are. The conservation is shown in bits and the aa are shaded according to their properties. A different graphical view of multiply aligned sequences is by a tree relating their sequence similarity. A way to estimate the significance of a tree is by bootstrap values.