SIM is a program which finds a user-defined number of best non-intersecting alignments between two protein sequences or within a sequence.

COBALT computes a multiple protein sequence alignment using conserved domain and local sequence similarity information.

Match-Box software proposes protein sequence multiple alignment tools based on strict statistical criteria. The method circumvents the gap penalty requirement: in the Match-Box method, gaps are the result of the alignment and not a governing parameter of the matching procedure. A reliability score is provided below each aligned position. The Match-Box program is particularly suitable for finding and aligning conserved structural motives, in particular in protein core.

This program takes as input a protein sequence and a multiple alignment of a protein family and computes a jumping alignment of the sequence and the alignment.

Alignment Annotator is a web application to create interactive annotated sequence alignments including coupled OpenAstex based 3D visualization.

Pfaat is a Java application that allows one to edit, analyze, and annotate multiple sequence alignments. The annotation features are a key component as they provide a framework to for further sequence, structure and statistical analysis.

Excel-based Protein alignment software.