algorithm based on progressive alignment, and it offers various multiple alignment strategies. First, MAFFT constructs a distance matrix based on the number of shared 6-tuples. Second, it builds the guide tree based on the previous matrix. Third, it clusters the sequences with the help of the Fast Fourier Transform and starts the alignment. Based on the new alignment, it reconstructs the guide tree and align again. Phylogenetic analysis To perform phylogenetic analysis, the first step is to reconstruct the phylogenetic tree: given a collection of species, the problem is to reconstruct or infer the ancestral relationships among the species, i.e., the phylogenetic tree among the species. Distance matrix methods perform this activity. Distance matrix methods Distance matrix methods of phylogenetic analysis explicitly rely on a measure of "genetic distance" between the sequences being classified, and therefore require multiple sequences as an input. Distance methods attempt to construct an all-to-all matrix from the sequence query set describing the distance between each sequence pair. From this is constructed a phylogenetic tree that places closely related sequences under the same interior node and whose branch lengths closely reproduce the observed distances between sequences. Distance-matrix methods may produce either rooted or unrooted trees, depending on the algorithm used to calculate them. Given species, the input is an distance matrix where is the mutation distance between species and . The aim is to output a tree of degree which is consistent with the distance matrix. They are frequently used as the basis for progressive and iterative types of multiple sequence alignment. The main disadvantage of distance-matrix methods is their inability to efficiently use information about local high-variation regions that appear across multiple subtrees. Despite potential problems, distance methods are extremely fast, and they often produce a reasonable estimate of phylogeny. They also have certain benefits over the methods that use characters directly. Notably, distance methods allow use of data that may not be easily converted to character data, such as DNA-DNA hybridization assays. The following are distance based methods for phylogeny reconstruction: Additive tree reconstruction UPGMA Neighbor joining Fitch-Margoliash Additive tree reconstruction Additive tree reconstruction is based on additive and ultrametric distance matrices. These matrices have a special characteristic: Consider an additive matrix . For any three species the corresponding tree is unique. Every ultrametric distance matrix is an additive matrix. We can observe this property for the tree below, which consists on the species