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AMAS - Analyse Multiply Aligned Sequences
http://barton.ebi.ac.uk/servers/amas_server.html

Block Maker finds conserved blocks in a group of two or more unaligned protein sequences, which are assumed to be related, using wo different algorithms.
http://blocks.fhcrc.org/blockmkr/make_blocks.html

BOXSHADE 3.21, Pretty Printing and Shading of Multiple-Alignment files
http://www.ch.embnet.org/software/BOX_form.html

Clustalw - EMBL Outstation, European Bioinformatics Institute.
http://www2.ebi.ac.uk/clustalw/

CODEHOP: COnsensus-DEgenerate Hybrid Oligonucleotide Primers.PCR primers designed from protein multiple sequence alignments. The program is intended for cases where the protein sequences are distant from each other and degenerate primers are needed.
http://blocks.fhcrc.org/blocks/codehop.html

DIALIGN constructs pairwise and multiple alignments by comparing whole segments of the sequences.
http://bibiserv.techfak.uni-bielefeld.de/dialign/

LAMA (Local Alignment of Multiple Alignments) is a program for comparing protein multiple sequence alignments with each other. LAMA compares multiple sequence alignments of proteins. If you have only a single protein sequence you first need to find other
http://blocks.fhcrc.org/blocks-bin/LAMA_search.sh

MATCH-BOX - Simultaneous alignment of several protein sequences where each aligned position is weighted by a reliability score.
http://www.fundp.ac.be/sciences/biologie/bms/matchbox_submit.html

MBS-Aligner / CLUSTALW simple and customizable interface.
http://mbshortcuts.com/mbsalign/

Multiple Alignment, GeneBee services
http://www.genebee.msu.su/services/malign_reduced.html

Multiple sequence alignment by Florence Corpet
http://www.toulouse.inra.fr/multalin.html

Musca - multiple sequence alignment algorithm.
http://cbcsrv.watson.ibm.com/Tmsa.html

MVIEW: view Blast results as a multiple alignment
http://bioweb.pasteur.fr/seqanal/interfaces/mview_blast-simple.html

SAM - Sequence Alignment and Modeling System.
http://www.cse.ucsc.edu/research/compbio/sam.html

Sequence Logos - A sequence logo is a graphical representation of aligned sequences where at each position the size of each residues proportional to its frequency in that position and the total height of all the residues in the position is proportional.
http://www.bio.cam.ac.uk/cgi-bin/seqlogo/logo.cgi

treealign: phylogenetic alignment of homologous sequences
http://bioweb.pasteur.fr/seqanal/interfaces/treealign.html

VISTA - VISualization Tool for Alignments. VISTA is an integrated system for global alignment and visualization, designed for comparative genomic analysis.
http://www-gsd.lbl.gov/vista/vista_web.htm