multiple sequence alignment

Dear Sir,

Thanks alot.

My questions are:

1.Is it mandatory to align equal sized sequences when aligning them or it is possible to align short with full length sequences?

2.Does deleting gaps affects the aligned sequences?

3.How to know the gap or residue is due to artifact?

4.How to know the quality of the alignment?

5.How to measure identity % distances among different sequences?example see table1 page 2455.

Best Regards