X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Ftree.html;fp=help%2Fhtml%2Fcalculations%2Ftree.html;h=6a31403ce6e4674293a52413db463eced16478b3;hb=cd33c321daf37cdd0d67e9745fc699aa9e7fc103;hp=b223b0b7189a4f4bfbe5865ada6ea3f225a9e75b;hpb=e1f1933f8038dd46960bf5c564e37de8211732ae;p=jalview.git
diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html
index b223b0b..6a31403 100755
--- a/help/html/calculations/tree.html
+++ b/help/html/calculations/tree.html
@@ -33,21 +33,26 @@ 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, 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.
+
+
+
+ - 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.
+
- Sequence Feature Similarity
Trees
are constructed from a distance matrix formed from Jaccard
distances between sequence features observed at each column of the
@@ -68,7 +73,6 @@ between each pair of sequences in the alignment :
same type will be grouped together in trees computed with this
metric. This measure was introduced in Jalview 2.9
-
Tree Construction Methods
Jalview currently supports two kinds of agglomerative clustering
methods. These are not intended to substitute for rigorous
@@ -89,7 +93,6 @@ phylogenetic tree construction, and may fail on very large alignments.
expensive than UPGMA.
-
A newly calculated tree will be displayed in a new tree viewing window. In
addition, a new entry with the same tree viewer window name will be added in the Sort