X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=00a2ec405971542b021a483760a965ebf40be132;hb=5160a2b12eaed0e6fb398ec3ff3805e1630b9b83;hp=00bca80edc6a3ebefd460129804c9db33f2c8024;hpb=c973cc268cbba93fa4ca9620c3910d30891a5abc;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 00bca80..00a2ec4 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,176 +1,657 @@ - -
Alignment Menu
----
-- Undo
-
- This will undo any edits you make to the alignment. This applies to insertion - or deletion of gaps, cutting residues or sequences from the alignment, pasting -- Redo
-
-- Cut
-- Copy
-- Paste -
--
-- To New Alignment
-- Add To This Alignment
-- Delete
-- Select All
-- Deselect All
-- Invert Selection
-- Undefine Groups
-- Remove Left
-- Remove Right
-- Remove Empty Columns
-- Remove All Gaps
-- Remove Redundancy
-- Pad Gaps
-
---
-- Find
-
---
-- Font
-- Wrap
-- Show Full Sequence ID
-- Boxes
-- Text
-- Colour Text
-- Show Gaps
-- Show Annotations
-- Sequence Features
-- Overview Window
-
---
-- Apply Colour To All Groups
-- None
-- ClustalX
-- Blosum62 Score
-- Percentage Identity
-- Zappo
-- Taylor
-- Hydrophobicity
-- Helix Propensity
-- Strand Propensity
-- Turn Propensity
-- Buried Index
-- Nucleotide
-- User Defined
-- By Conservation
-- Modify Conservation Threshold
-- Above Identity Threshold
-- Modify Identity Threshold
-
-- - + + + +-
-- Sort -
--
-- by ID
-- by Group
-- by Pairwise Identity
-- Calculate Tree -
--
-- Average Distance Using % Identity
-- Neighbour Joining Using % Identity
-- Average Distance Using Blosum62
-- Neighbour Joining Using Blosum62
-- Paiwise Alignments
-- Principal Component Analysis
-- Web Service -
--
-- Clustal Alignment
-- JPred
-- Muscle Alignment
--
+ Alignment Window Menus +
+Selecting items from the following submenus will start a + remote service on compute facilities at the University of Dundee, + or elsewhere. You need a continuous network connection in order to + use these services through Jalview.
+