X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=00a2ec405971542b021a483760a965ebf40be132;hb=5160a2b12eaed0e6fb398ec3ff3805e1630b9b83;hp=24f823974882b16687a543dc217fbc542fbc527f;hpb=f3226d82fed697cb41c626a5204bb3b56add70c3;p=jalview.git
diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index 24f8239..00a2ec4 100755
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -244,7 +244,7 @@
Selects all the sequences and residues in the
alignment.
Use <CTRL> and A (<APPLE>
and A on a MacOSX) to select all.
-
+
Deselect All (Escape)
Removes the current selection box (red dashed box) from
the alignment window. All selected sequences, residues and
@@ -279,12 +279,11 @@
columns in the alignment according to secondary structure,
labels and values shown in alignment annotation rows.
Select Highlighted Columns
Selects
- the columns currently highlighted as a result of a find, mouse
- over, or selection event from a linked structure viewer or other
- application. Modifiers will work on some platforms: SHIFT will
- add columns to selection, ALT will invert the highlighted set
- before selection, and CTRL (or META) will toggle the selection.
-
+ the columns currently highlighted as a result of a find, mouse
+ over, or selection event from a linked structure viewer or other
+ application. Modifiers will work on some platforms: ALT will add
+ all but the highlighted set to the column selection, and CTRL
+ (or META) will toggle the selection.
View
@@ -313,7 +312,7 @@
or hide sequence features on this alignment.
Sequence
- Feature Settings...
Opens the
+ Feature Settings...
Opens the
Sequence Feature Settings dialog box to control the colour
and display of sequence features on the alignment, and
configure and retrieve features from DAS annotation
@@ -428,12 +427,12 @@
If this box is selected then the sequence names
displayed in the sequence label area will be aligned
against the left-hand edge of the alignment display,
- rather than the left-hand edge of the alignment window.
+ rather than the left-hand edge of the alignment window.
Show Hidden Markers
When this box is selected, positions in the
alignment where rows and columns are hidden will be
- marked by blue arrows.
+ marked by blue arrows.
Boxes
If this is
selected the background of a residue will be coloured
using the selected background colour. Useful if used in
@@ -462,7 +461,6 @@
symbols will be rendered as a '.', highlighting
mutations in highly conserved alignments.
-
@@ -542,44 +540,26 @@
viewer window.
- Calculate Tree
Functions
- for calculating trees on the alignment or the currently
- selected region. See calculating
- trees.
-
-
- - Neighbour Joining Using PAM250
- - Neighbour Joining Using Sequence
- Feature Similarity
- - Neighbour Joining Using Blosum62
- - Neighbour Joining Using % Identity
- - Average Distance Using PAM250
- - Average Distance Using Sequence
- Feature Similarity
- - Average Distance Using Blosum62
- - Average Distance Using % Identity
-
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.
+ Calculate Tree or PCA ...
Opens the
+ calculations dialog for
+ for calculating trees or
+ principle component analysis
+ plots on the alignment or the currently selected
+ region.
- Principal Component Analysis
Shows
- a spatial clustering of the sequences based on similarity
- scores calculated with the alignment. See Principal
- Component Analysis.
-
- Extract Scores ... (optional)
This
- option is only visible if Jalview detects one or more
- white-space separated values in the description line of the
- alignment sequences.
When selected, these numbers are
- parsed into sequence associated annotation which can then be
- used to sort the alignment via the Sort by→Score menu.
-
- Autocalculate Consensus
For
+ Pairwise Alignments
Applies
+ Smith and Waterman algorithm to selected sequences. See pairwise
+ alignments.
+
+ Extract Scores ... (optional)
This
+ option is only visible if Jalview detects one or more
+ white-space separated values in the description line of the
+ alignment sequences.
When selected, these numbers are
+ parsed into sequence associated annotation which can then be
+ used to sort the alignment via the Sort by→Score menu.
+
+ Autocalculate Consensus
For
large alignments it can be useful to deselect
"Autocalculate Consensus" when editing. This
prevents the sometimes lengthy calculations performed after
@@ -615,7 +595,7 @@
in Jalview 2.8.1
'Standard Databases' will check sequences against
- the EBI databases plus any active DAS sequence sources<
+ 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.
@@ -639,22 +619,22 @@
- JPred Secondary Structure Prediction
Secondary structure prediction by network
- consensus. See the Jpred3
+ consensus. See the Jpred
client entry for more information. The behaviour of this
calculation depends on the current selection:
- If nothing is selected, and the displayed
- sequences appear to be aligned, then a JNet prediction
+ sequences appear to be aligned, then a JPred prediction
will be run for the first sequence in the alignment,
using the current alignment. Otherwise the first
sequence will be submitted for prediction.
- If just one sequence (or a region on one
sequence) has been selected, it will be submitted to
- the automatic JNet prediction server for homolog
+ the automatic JPred prediction server for homolog
detection and prediction.
- If a set of sequences are selected, and they
appear to be aligned, then the alignment will be used
- for a Jnet prediction on the first
+ for a JPred prediction on the first
sequence in the set (that is, the one that appears
first in the alignment window).