Multiple Sequence Alignment Web Service

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Fmsaclient.html;h=775eec89a63f1c6c63bb139b2e6075d969c1388b;hb=1b9fc500a75a38d7c4408d4b209384d5236911cc;hp=7f4bac9128624af36f724c6f0c48376d82510943;hpb=c53aeee9a688f68d64106a968876e542f701fbc6;p=jalview.git diff --git a/help/html/webServices/msaclient.html b/help/html/webServices/msaclient.html index 7f4bac9..775eec8 100644 --- a/help/html/webServices/msaclient.html +++ b/help/html/webServices/msaclient.html @@ -1,54 +1,75 @@ 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 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

JABAWS framework

'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 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 Multiple Sequence Alignment +sub jobs running at once + +