X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2Falwcalculate.html;h=eae9c92490347f8b7ee758a4030ec572a61e531e;hb=2b3bd506ee1cc2d1a26a3425ccba48665179a9fb;hp=5a972969b41a2126b33b3d3326747b2c0ae0ae65;hpb=8c0737632c158907098990b81ac702710721e9f2;p=jalview.git
diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html
index 5a97296..eae9c92 100755
--- a/help/html/menus/alwcalculate.html
+++ b/help/html/menus/alwcalculate.html
@@ -1,55 +1,81 @@
-
-Alignment Window Menus
-
-
-Alignment Window Calculate Menu
-Calculate
-
- - Sort
-
- - by ID
- This will sort the sequences according to sequence name. If the sort is
- repeated, the order of the sorted sequences will be inverted.
- - by Group
- This will sort the sequences according to sequence name.
- If the sort is repeated, the order of the sorted sequences will be inverted.
-
- - by Pairwise Identity
- This will sort the selected sequences by their percentage
- identity to the consensus sequence. The most similar sequence is put at
- the top.
- - The Sort menu will have
- some additional options if you have just done a multiple alignment calculation,
- or opened a tree viewer window.
-
-
-
- - Calculate Tree
- Functions for calculating trees on the alignment or the currently selected
- region. See calculating trees.
-
- - Average Distance Using % Identity
- - Neighbour Joining Using % Identity
- - Average Distance Using Blosum62
- - Neighbour Joining Using Blosum62
-
-
-
- - 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 Component
- Analysis.
-
- - Autocalculate Consensus
- For large alignments it can be useful to deselect "Autocalculate
- Consensus" when editing. This prevents lengthy calculations which are
- performed after each sequence edit.
-
-
-
-
+
+
+Alignment Window Menus
+
+
+Alignment Window Calculate Menu
+
+ - Sort
+
+ - by ID
+ This will sort the sequences according to sequence name. If the sort is
+ repeated, the order of the sorted sequences will be inverted.
+ - by Length
+ This will sort the sequences according to their length (excluding gap characters). If the sort is
+ repeated, the order of the sorted sequences will be inverted.
+ - by Group
+ This will sort the sequences according to sequence name.
+ If the sort is repeated, the order of the sorted sequences will be inverted.
+
+ - by Pairwise Identity
+ This will sort the selected sequences by their percentage
+ identity to the consensus sequence. The most similar sequence is put at
+ the top.
+ - The Sort menu will have
+ some additional options if the alignment has any associated
+ score annotation, or you have just done a multiple alignment calculation
+ or opened a tree viewer window.
+
+
+
+ - Calculate Tree
+ Functions for calculating trees on the alignment or the currently selected
+ region. See calculating trees.
+
+ - Average Distance Using % Identity
+ - Neighbour Joining Using % Identity
+ - Average Distance Using Blosum62
+ - Neighbour Joining Using Blosum62
+
+
+
+ - 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 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 large alignments it can be useful to deselect "Autocalculate
+ Consensus" when editing. This prevents the sometimes lengthy calculations
+ performed after each sequence edit.
+
+
+
+