CLUSTALW

ClustalW is a software package for multiple alignment (implementing an algorithm of Thompson, Higgins, Gibson 1994 [4]). The basic idea is the same as in the Feng-Doolittle algorithm:

1.

Calculate the $k \choose 2$ pairwise alignment scores, and convert to two distances.

2.

Use clustering algorithm (Neighbor-Joining) to build a tree from the distances.

3.

align sequence - sequence, sequence - profile, profile - profile in decreasing similarity order.

This algorithm makes use of many ad-hoc rules such as weighting, different matrix scores and special gap scores.