X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2Falwcalculate.html;h=c7a1c87c9c005b8a5c8b5f14265ac4f8be54d305;hb=806c9dc4a3d841fe36e7d17ab45d783a9fc95f26;hp=80323487a675e09f4129dc01495e27b24ff97c01;hpb=dde303bc73617ab4eb3e681e67cf899e6a971318;p=jalview.git
diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html
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@@ -53,37 +53,19 @@
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
-
+ 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.
- Principal Component Analysis
Shows
- a spatial clustering of the sequences based on similarity scores
- calculated over 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