ClustalW2 is a MSA program designed strictly for the analysis of proteins or DNA, not RNA. It is hosted by the European Bioinformatics Institute (EBI) and is provided as either a webpage form or downloaded as a software package. It is one of the most widely used MSA softwares, with many newer ones written based on ClustalW, the original version. ClustalW2 allows scientists to input up to 500 or 10 MB of sequences in formats such as FASTA, RSF, EMBL, Swiss-prot (or UniProtKB, EMBL) and GDE. A range of analysis options is available; for example, the user has the option to run "full" or "fast" alignments, generate "interactive" or "email" results, and produce only MSAs or also phylogenetic trees (a diagram depicting evolutionary relationships).
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
United Kingdom
011-44-1223-494-444
ebi.ac.uk
Also a highly popular MSA software hosted by EBI, T-Coffee enables the user to use sequences obtained from a variety of sources (e.g., Blast, Fast), or alignments from different programs (such as ClustalW2, Dialign).T-Coffee combines whatever is provided and generates a completely new MSA with the closest and most accurate match between the various formats. The user can choose between using statistical tools known as scoring matrices (such as PAM or BLOSSUM) to analyze the results of the MSA, which are a statistical method of determining the presence of an alignment between sequences, and determine if this alignment is significant or simply an artifact.
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
United Kingdom
011-44-1223-494-444
ebi.ac.uk
SAM is a multiple-sequence aligner for proteins that enables any type of protein structure (e.g., beta strand, alpha helix, coil) to be determined from an alignment of sets of protein sequences. These sequences can then be used to see if proteins are related (i.e., they are homologs), if the homologs have been structurally validated and which organisms they may have come from. SAM uses the Hidden Markov Model, a complex statistical model widely used in biology, as the basis of its algorithm.
Biomolecular Engineering
University of California, Santa Cruz
Santa Cruz, CA 95064
soe.ucsc.edu
831-459-4250