Iterative-Progressive-MSA Tool

IPAS is a new and practial iterative progressive multiple sequence alignment algorithm, used to align protein sequences, which is a close variant of the MUSCEL algorithm. However, based on the gene sequences length, our algorithm starts either with the "kmer" distance table or with the "Dynamic Programming (DP)" distance table. The other steps of this algorithm include: generating a Guide-tree using UPGMA, multiple sequence alignments, "kimura" distance calculation from aligned sequences and new techniques to improve multiple sequence alignments. Assessed on BAliBASE 3.0, PREFAB 4.0,SABMARK 1.65, and OXBENCH, IPAS gives accurate alignment compared to the existing well known methods: T-Coffee, MUSCEL, and MAFFT.