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Mafft [150] is a multiple sequence alignment algorithm with different
characteristics that provides an alternative to calling ClustalW.
PhylogeneticTree creates JPG images from phylogenetic tree data.
These services provide quite common functionality in the sense that equiv-
alent or similar services are also offered by other service providers. Most of
the other services of the Web API are more DDBJ-specific.
3.2.2 Basic Multiple Sequence Alignment Workflow
In the simplest case, an alignment workflow in Bio-jETI consists of a SIB
that calls an alignment service, and some SIBs that take care of handling the
input and output data. Figure 3.6 shows such a basic alignment workflow: the
first SIB (at the left, with the underlined name) lets the user select a file from
the local file system, its content is then read into the execution context, the
data is sent to the DDBJ's ClustalW web service for alignment computation,
and finally the result is displayed.
Fig. 3.6 Basic alignment workflow, using the DDBJ's ClustalW web service
If an error occurs during execution of any service, an error message is
written to the execution context by the respective SIB. This message can
simply be displayed by the ShowMessageDialog SIB, or handled specifically,
for instance by modeling fault tolerance or graceful termination of the com-
putation with the possibility of resuming the workflow execution at the failed
step later on. Note that in the example workflows that are shown here, all
error handling is delegated to the calling workflow (by defining the error
branches of the SIBs as model branches) to facilitate reading.
3.2.3 Variations of the Basic Workflow
Figure 3.7 shows a Bio-jETI workflow canvas with several preconfigured (i.e.,
with parameters already set) workflow snippets. In detail, they provide the
following functionality:
1. Selecting and reading a sequence file from the local file system.
2. Calling the DDBJ's ClustalW alignment service.
3. Showing an alignment in a simple text dialog window.
4. Calling the DDBJ's Mafft alignment service.
 
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