ClustalW
ClustalW is still a popular, progressive multiple sequence alignment tool [Thompson et al., 1994], 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.
Figure 2.2: Setting ClustalW alignment parameters
ClustalW produces two outputs: an alignment and a tree. An example of an alignment made using ClustalW is shown in figure 2.3.
Figure 2.3: Output of ClustalW alignment with the "Show annotations" option in the Side Panel enabled.