ArrayList<DNASequence> dnaSeqs = new ArrayList<DNASequence>();
try {
	dnaSeqs.add(new DNASequence("ATAGAGCGGCCGCCACCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGGGTCTTKAAGGGGGGTT",AmbiguityDNACompoundSet.getDNACompoundSet()));
        dnaSeqs.add(new DNASequence("ATAGAGCGGCCGCCACCGCTGAGCATACTAGCATAACCCCTTGGGGCTCTAACGGGTCTTGAGGGTTTTT",AmbiguityDNACompoundSet.getDNACompoundSet()));
        dnaSeqs.add(new DNASequence("TAATAGAGCGGCCGCCACCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGGTCTTGAGGGGTTTTTTGCTGAAAGGAGGAACTAT",AmbiguityDNACompoundSet.getDNACompoundSet()));           
} catch (CompoundNotFoundException e) {
	e.printStackTrace();
}
Profile<DNASequence, NucleotideCompound> profile = Alignments.getMultipleSequenceAlignment(dnaSeqs);
System.out.println(profile);

biojava output:
--ATAGAGCGGCCGCCACCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGGGTCTTKAAGGGGGGTT----------------------
--ATAGAGCGGCCGCCACCGCTGAGCAT--ACTAGCATAACCCCTTGGGGC-TCTAAC--GGGTCTTGA----GGGTTTTT-------------------
TAATAGAGCGGCCGCCACCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGG-TCTTGA---GGGGTTTTTTGCTGAAAGGAGGAACTAT

clustalx output:
--ATAGAGCGGCCGCCACCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGGGTCTTKAAGGGGGGTT-------------------
--ATAGAGCGGCCGCCACCGCTGAGCAT--ACTAGCATAACCCCTTGGGG-CTCT-AACGGG-TCTTGAGGG-TTTTT-------------------
TAATAGAGCGGCCGCCACCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGG-TCTTGAGGGGTTTTTTGCTGAAAGGAGGAACTAT
  *************************:  ******************** **** ****