X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Fmsaclient.html;h=d627c66e09d132d4bc5ff0a1951215e4ccad4e6c;hb=6f9d7b98943ecba292a9c0dd65b30c4d8150c98f;hp=775eec89a63f1c6c63bb139b2e6075d969c1388b;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git diff --git a/help/html/webServices/msaclient.html b/help/html/webServices/msaclient.html index 775eec8..d627c66 100644 --- a/help/html/webServices/msaclient.html +++ b/help/html/webServices/msaclient.html @@ -1,76 +1,90 @@ + --> 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: -

- 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.

-

+ 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: +

+ 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. +

+

-

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 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 +
+

+
+ +
+