CLUSTALW
CLUSTALW is a fully automatic program for global multiple alignment of DNA and protein sequences. The alignment is progressive and considers sequence redundancy. Trees can also be calculated from multiple alignments. The program has some adjustable parameters with reasonable defaults.
INPUT = dna sequence files; protein sequence files; profiles
Manual: http://www.ebi.ac.uk/2can/tutorials/nucleotide/clustalw1.html
Test input file (for creating an alignment): clustal_test_in1.fasta
Test output file1 (aligned sequnces): clustal_test1_out1.aln
Test output file2 (tree): clustal_test_out2.dnd
