Multiple Sequence Alignment Web Service

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2FwebServices%2Fmsaclient.html;h=775eec89a63f1c6c63bb139b2e6075d969c1388b;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=6fea43e7ea898cf48a9620a47359797748efc854;hpb=e3f4349374e532d0f9bb2bc163ff1783ca030fd6;p=jalview.git diff --git a/help/html/webServices/msaclient.html b/help/html/webServices/msaclient.html index 6fea43e..775eec8 100644 --- a/help/html/webServices/msaclient.html +++ b/help/html/webServices/msaclient.html @@ -1,38 +1,76 @@ - - -Multiple Sequence Alignment Web Service - - -Multiple Sequence Alignment Web Services -

-Multiple sequence alignment services are accessed from the Web -Service→Alignment menu. When an entry from this menu 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 existing alignments in the input are passed to the service -for profile based alignment. -

-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

- - + + + +Multiple Sequence Alignment Web Service + + +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 + 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.
Versions shown are those bundled with JABAWS 2.01 - if you are using a different server, check its home page to find out which versions are provided.

Clustal Omega and Clustal W (version 2.0.12)
Mafft (version 6.8.57b)
Muscle (version 3.8.31)
Tcoffee (version 8.99)
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 Multiple Sequence Alignment +sub jobs running at once + +

+ +