CINEMA is a Colour INteractive Editor for Multiple Alignments.

Online tool to calculate a consensus for the CLUSTAL or MSF multiple alignment.

Multiple alignment by sequence annealing

Multiple Sequence Alignment Software. With STRAP you can align your proteins by sequence and 3D-structure. The free computer program STRAP supports the analysis of hundreds of proteins and integrates amino acid sequence, secondary structure, 3D-structure and genomic- and mRNA-sequence and residue annotation.

Online tools that pastes X positions left and/or right of the alignment from each of the involved sequences in a CLUSTAL (with accession) multiple alignment.

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

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.