Protein multiple sequence alignment is an important bioinformatics tools. 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 distance is proposed to evaluate several protein multiple sequence alignment algorithms that are widely used currently. As the permutation distance 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. In addition

the longest common subsequence method can well define the distances between different permutations. Using these methods

we compared and assessed Dialign

Tcoffee

ClustalW and Muscle.