X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Fmsaclient.html;h=2fbbdbcfb61a056fe94624304cd38bfa9af742c9;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=d35a28e66c0d26056cb9220865e1bd6e67b9fe06;hpb=05c695da50cc7ac1bd759ed5c58b3d5d7a9d0085;p=jalview.git diff --git a/help/html/webServices/msaclient.html b/help/html/webServices/msaclient.html index d35a28e..2fbbdbc 100644 --- a/help/html/webServices/msaclient.html +++ b/help/html/webServices/msaclient.html @@ -1,55 +1,93 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> 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:

-

-

-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 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 2.01 - 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 +
+

+
+ +
+