ClustalW

ClustalW is still a popular, progressive multiple sequence alignment tool [Thompson et al., 1994] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7984417), despite being substantially older than ClustalO.

ClustalW has a single option: Guide Tree Algorithm: Select Normal or Quick. Quick uses a fast, but not as accurate algorithm for the alignment guide tree.

Image externalalignment_ClustalW_step2
Figure 2.3: Setting ClustalW alignment parameters

ClustalW produces two outputs: an alignment and a tree. An example of an alignment made using Clustal" is shown in figure 2.3.

Image clustal_output-web
Figure 2.4: Output of ClustalW alignment with the "Show annotations" option in the Side Panel enabled.