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-
-
-
-Tree Calculation
-
-
-
- Calculation of trees from alignments
-
-
- Trees are calculated on either the complete alignment, or just the
- currently selected group of sequences, via the calculations dialog opened from the Calculate→Calculate
- Tree or PCA... menu entry. 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.
-
-
-
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.
-
-
-
-
-