Tree Calculation

From: jprocter Date: Tue, 8 May 2007 16:50:28 +0000 (+0000) Subject: PID distance measure and finishing sentence. X-Git-Tag: Release_2_3~28 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=cf1d95b1485a70f76f58af1e2d7827dbd0f94014;p=jalview.git PID distance measure and finishing sentence. --- diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html index 47cac5b..1e2e0d0 100755 --- a/help/html/calculations/tree.html +++ b/help/html/calculations/tree.html @@ -1,62 +1,66 @@ - -Tree Calculation - -

Calculation of trees from alignments

Trees are calculated on either the complete alignment, or just the -currently selected group of sequences, using the functions in the -Calculate→Calculate tree submenu. There are -four different calculations, using one of two distance measures and -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. -
BLOSUM62
The sum of BLOSUM62 scores for the -residue pair at each aligned position. -

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. -

UPGMA tree
- UPGMA stands for Unweighted Pair-Group Method using Arithmetic - averages. Clusters are iteratively formed and extended by finding a - non-member sequence with the lowest average dissimilarity over the - cluster members. -
-
Neighbour Joining tree
- First described in 1987 by Saitou and Nei, this method applies a - greedy algorithm to find the tree with the shortest branch - lengths.
- This method, as implemented in Jalview, is considerably more - 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 -menu so that the alignment can be reordered to reflect the ordering of -the leafs of the tree. If the tree was calculated on a selected region -of the alignment, then the title of the tree view will reflect this.

- -

External Sources for Phylogenetic Trees

A number of programs exist for the reliable construction of - phylogenetic trees, which can cope with large numbers of sequences, - use better distance methods and can perform bootstrapping. Jalview - can read Newick - format tree files using the 'Load Associated Tree' entry of the - alignment's File menu. Sequences in the alignment will be - automatically associated to nodes in the -

- - - - + +Tree Calculation + +

Calculation of trees from alignments

Trees are calculated on either the complete alignment, or just the +currently selected group of sequences, using the functions in the +Calculate→Calculate tree submenu. There are +four different calculations, using one of two distance measures and +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

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. +

UPGMA tree
+ UPGMA stands for Unweighted Pair-Group Method using Arithmetic + averages. Clusters are iteratively formed and extended by finding a + non-member sequence with the lowest average dissimilarity over the + cluster members. +
+
Neighbour Joining tree
+ First described in 1987 by Saitou and Nei, this method applies a + greedy algorithm to find the tree with the shortest branch + lengths.
+ This method, as implemented in Jalview, is considerably more + 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 +menu so that the alignment can be reordered to reflect the ordering of +the leafs of the tree. If the tree was calculated on a selected region +of the alignment, then the title of the tree view will reflect this.

+ +

External Sources for Phylogenetic Trees

A number of programs exist for the reliable construction of + phylogenetic trees, which can cope with large numbers of sequences, + use better distance methods and can perform bootstrapping. Jalview + can read Newick + format tree files using the 'Load Associated Tree' entry of the + alignment's File menu. Sequences in the alignment will be + automatically associated to nodes in the tree, by matching Sequence + IDs to the tree's leaf names. +

+ + + +