Protein multiple sequence alignment is an important bioinformatics tool. It has important applications in biological evolution analysis and protein structure prediction. A variety of alignment algorithms in this field have achieved great success. However, each algorithm has its own inherent deficiencies. In this paper, permutation similarity is proposed to evaluate several protein multiple sequence alignment algorithms that are widely used currently. As the permutation similarity method only concerns the relative order of different protein evolutionary distances, without taking into account the slight difference between the evolutionary distances, it can get more robust evaluations. The longest common subsequence method is adopted to define the similarity between different permutations. Using these methods, we assessed Dialign, Tcoffee, ClustalW and Muscle and made comparisons among them. (C) 2010 Elsevier Inc. All rights reserved.