Motalign: A Multiple Sequence Alignment Algorithm Based on a New Distance and a New Score Function

In this paper, we present our new progressive alignment algorithm, called Motalign, for Multiple Sequence Alignment (MSA). Our algorithm adopts a new profile based distance [1] to compare two biological sequences and a new score function, called gPSP, to align profiles. We benchmarked our algorithm on different benchmarks. We compared the results obtained by our algorithm to those obtained by other ones, like CLUSTALW2, MUSCLE and MAFFT, by using the Column Score (CS) [2] and the Sum of Pairs Score (SPS) [2]. We obtained interesting results.