X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=fdaa0233478ea7509f25278b8f387d8b0ec88dcb;hb=1b9fc500a75a38d7c4408d4b209384d5236911cc;hp=d53b3eb799f7436865dd10a3e904bf9710db5549;hpb=bda1b6a4412a73727de4613cfe3a6829b0fe0804;p=jalview.git
diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index d53b3eb..fdaa023 100755
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -1,7 +1,7 @@
Alignment Window Menus
@@ -483,14 +484,15 @@
Neighbour Joining Using Blosum62
+ Note: Since Version 2.8.1, a number of additional similarity measures for tree calculation are provided in this menu.
Pairwise Alignments
Applies
Smith and Waterman algorithm to selected sequences. See pairwise alignments.
Principal Component Analysis
Shows
- a spatial clustering of the sequences based on the BLOSUM62 scores
- in the alignment. See Principal
+ a spatial clustering of the sequences based on similarity scores calculated with
+ the alignment. See Principal
Component Analysis.
Extract Scores ... (optional)
This
@@ -508,28 +510,36 @@
Sort With New Tree
When
enabled, Jalview will automatically sort the alignment when a new
tree is calculated or loaded onto it.
-
+ Show Flanking Regions
Opens
+ a new alignment window showing any additional sequence data either
+ side of the current alignment. Useful in conjunction with 'Fetch
+ Database References' when the 'Trim Retrieved Sequences' option is
+ disabled to retrieve full length sequences for a set of aligned
+ peptides.
+
Web Service Menu
This menu
is dynamic, and may contain user-defined web service entries in
addition to any of the following ones:
- Fetch DB References
This
- will use any of the database services that Jalview is aware of
- (e.g. DAS sequence servers and the WSDBFetch service provided by
- the EBI) to verify the sequence and retrieve all database cross
- references and PDB ids associated with all or just the selected
- sequences in the alignment.
'Standard Databases' will check
- sequences against the EBI databases plus any active DAS sequence
- sources, or you can verify against a specific source from one of
- the sub-menus.
- - Envision2 Services
Submits one or
- more sequences, sequence IDs or database references to analysis
- workflows provided by the EnVision2 web
- application. This allows Jalview users to easily access the EnCore
- network of databases and analysis services developed by members of
- ENFIN.
+ submenu contains options for accessing any of the database services
+ that Jalview is aware of (e.g. DAS sequence servers and the
+ WSDBFetch service provided by the EBI) to verify sequence start/end
+ positions and retrieve all database cross references and PDB ids
+ associated with all or just the selected sequences in the alignment.
+
+ - 'Trim Retrieved Sequences' - when checked, Jalview will
+ discard any additional sequence data for accessions associated with
+ sequences in the alignment.
Note: Disabling this
+ could cause out of memory errors when working with genomic
+ sequence records !
Added in Jalview 2.8.1
+
+ - 'Standard Databases' will check sequences against the EBI
+ databases plus any active DAS sequence sources<
+
Other sub-menus allow you to pick a specific source to query -
+ sources are listed alphabetically according to their nickname.
+
Selecting items from the following submenus will start a
remote service on compute facilities at the University of Dundee, or