+ 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.
Most alignment services are + provided by the + JABAWS framework, which allows you to + customise the precise parameters used when running each alignment + prgoram. 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
-
+
- ClustalW (version 2.0.12) +
- Mafft (version 6.713) +
- Muscle (version 3.7) +
- Tcoffee (version 8.14) +
- Probcons (version 1.12) +
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 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:
-
