X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwcalculate.html;h=1f0474a49b26007570ea5f7fec0275373dce3e85;hb=d305e02d8b425bb501141ad32142aeb8572adc57;hp=9d40868b3c59e930f4c9e8701fbb8405ffdb3a92;hpb=5a6d8d69732445af2189fc4bab7a09dbd77bb829;p=jalview.git
diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html
index 9d40868..1f0474a 100755
--- a/help/html/menus/alwcalculate.html
+++ b/help/html/menus/alwcalculate.html
@@ -1,54 +1,96 @@
-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.
+
+ - 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.
+
+
+