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diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html
index 9d40868..50bb37b 100755
--- a/help/html/menus/alwcalculate.html
+++ b/help/html/menus/alwcalculate.html
@@ -1,54 +1,104 @@
-Alignment Window Menus
+
+
+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 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 the sometimes lengthy calculations
- performed after each sequence edit.
-
-
-
+
+ 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.
+ - Translate as cDNA (not applet)
This option is visible for nucleotide alignments.
+ Selecting this option shows the DNA's calculated protein product in a new window. Note that the
+ translation is not frame- or intron-aware; it simply translates all codons in each sequence, using the
+ standard genetic code (any incomplete final codon is discarded).
+ You can perform this action on the whole alignment,
+ or selected rows, columns, or regions.
+ - Get Cross-References (not applet)
This option is visible where sequences have cross-references to
+ other standard databases; for example, an EMBL entry may have cross-references to one or more UNIPROT entries.
+ Select the database to view all cross-referenced sequences in a new window.
+ - 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.
+ - Sort Alignment With New Tree
If
+ this option is selected, the alignment will be automatically sorted
+ whenever a new tree is calculated or loaded.
+
+
+