X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fcalculations%2Ftree.html;h=a01c7bedacea89dede72184aab7232d3202082c6;hb=e5cbd35e13f46ae1d59a08b0af1086677418141d;hp=9591f3963b0079a9a508f6f2a06efdd0c3f9e9ca;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html
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--- a/help/html/calculations/tree.html
+++ b/help/html/calculations/tree.html
@@ -1,22 +1,24 @@
+ -->
Tree Calculation
Calculation of trees from alignments
@@ -31,17 +33,24 @@ constructing the tree from one of two algorithms :
Distance Measures
Trees are calculated on the basis of a measure of similarity
between each pair of sequences in the alignment :
-
-- PID
The percentage identity between the two
-sequences at each aligned position.- PID = Number of equivalent
-aligned non-gap symbols * 100 / Smallest number of non-gap positions
-in either of both sequences
This is essentially the 'number of
-identical bases (or residues) per 100 base pairs (or residues)'.
- - BLOSUM62
The sum of BLOSUM62 scores for the
-residue pair at each aligned position.
-
-
-Tree Construction Methods
+
+ - PID
The percentage identity between
+ the two sequences at each aligned position.
+
+ - PID = Number of equivalent aligned non-gap symbols * 100 /
+ Smallest number of non-gap positions in either of both sequences
+ This is essentially the 'number of identical bases (or
+ residues) per 100 base pairs (or residues)'.
+
+
+ - BLOSUM62, PAM250, DNA
These options
+ use one of the available substitution matrices to compute a sum of
+ scores for the residue pairs at each aligned position. For details
+ about each model, see the list of
+ built-in score matrices.
+
+
+ Tree Construction Methods
Jalview currently supports two kinds of agglomerative clustering
methods. These are not intended to substitute for rigorous
phylogenetic tree construction, and may fail on very large alignments.