ClustalW is a classical and popular multiple sequence alignment program,
while
ProbCons is a great program according to the
latest benchmark.
MUSCLE is another good and fast alignment algorithm. Jalview
can display alignments in a graphic interface and have lots of other functions, like phylogenetic tree
A tool to BLAST a group of query protein/DNA sequence against a group of target sequences. The results will be shown in an easily readable tabular form.