X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Ftree.html;h=038020fc33696d690251f5bb50d30a0a269c4d44;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=5ca9fcbd2dd78a09ea704d49a497a69fe91635f4;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git
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-Tree Calculation
+
+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.
-Once calculated, trees are displayed in a new tree viewing window. 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, 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.
-
-- 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.
+
+ 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. Once calculated, trees are displayed in a new tree viewing window. 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, 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
+ alignment.
+
+ - Similarity at column i = (Total number of
+ features displayed - Sum of number of features in common at i)
+
Similarities are summed over all columns and divided by
+ the number of columns.
Since the total number of
+ feature types is constant over all columns of the alignment,
+ we do not scale the matrix, so tree distances can be
+ interpreted as the average number of features that differ over
+ all sites in the aligned region.
+
-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.
+
Distances are computed based on the currently displayed feature
+ types. Sequences with similar distributions of features of the
+ 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 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.