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diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html
index 6ee7ed8..c7a1c87 100755
--- a/help/html/menus/alwcalculate.html
+++ b/help/html/menus/alwcalculate.html
@@ -1,55 +1,120 @@
-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 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.
-
- - 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 or PCA ...
Opens the
+ calculations dialog for
+ for calculating trees or
+ principle component analysis
+ plots on the alignment or the currently selected
+ region.
+
+
+ - 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.
+
+ - 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 split frame 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.
+
+ - Reverse, Reverse Complement (not applet)
+ These options are visible for nucleotide alignments.
+ Selecting them adds the reverse (or reverse complement) of the
+ sequences (or selected region) as new sequences in the
+ alignment. To try this out, add this sequence and perform
+ 'Reverse Complement' followed by 'Translate as cDNA':
+ Seq
+ GTCATTTGCGCGTGTTGATTATTCGGACCGCTCCACTTCCCTTTACTCGTGCGTTCAATTGATTTAATCCTC
+ TGGGGGGGCTCTGGTTTACATAGCTTAAATCTATTCCATTCAAGGAAGCTCATG
+
+ - 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 split
+ frame 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.
+ - 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.
+
+