Multiple Sequence Alignment Web Services

Multiple sequence alignment services are accessed from the Alignment submenu of the Alignment Window's Web Service menu. When an entry from one of these menus is selected, either the currently selected residues, or the whole sequence set (if there is no selection or only one sequence is selected) will be submitted for multiple sequence alignment.

There are two kinds of multiple sequence alignment operations available:

- alignment - where a new alignment is constructed from the input
- realignment - where any aligned sequences will be used by the service to construct a profile based alignment of the remaining unaligned sequences

JABAWS Alignment services
Most alignment services are provided by the JABAWS framework, which allows you to customise the precise parameters used when running each alignment program. In addition to the 'Default settings', you may choose from a range of alignment preset settings, or create your own using the 'Edit Settings And Run ..' dialog box.

Alignment programs supported by JABAWS.
Versions shown are those bundled with JABAWS 2.2 - if you are using a different server, check its home page to find out which versions are provided.

- Clustal Omega (version 1.2.4)
- ClustalW (version 2.1)
- Mafft (version 7.310)
- Muscle (version 3.8.31)
- T-coffee (version 11.00.8cbe486)
- Probcons (version 1.12)
- MSAProbs (version 0.9.7)
- GLProbs (version 0.9.7)

Multiple Alignments of Sequences with hidden columns
Multiple alignment services are 'column separable' analysis operations. If the input contains hidden columns then each visible segment of the input sequence set will be submitted for alignment separately, and the results concatenated (with the hidden regions preserved) once all alignment functions have completed. Each sub-job's state is reported in its own tab:

Multiple Multiple Sequence Alignment sub jobs running at once