Tree Calculation

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Ftree.html;h=59736ca8793dc5304a990b37248a8c080798434c;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=a8dbe592c67237fab7352903f789ed1b35dded84;hpb=998ae297436877c6086f657e0a02c376cb5eb4dd;p=jalview.git diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html index a8dbe59..59736ca 100755 --- a/help/html/calculations/tree.html +++ b/help/html/calculations/tree.html @@ -1,85 +1,130 @@ - -Tree Calculation - -

Calculation of trees from alignments

Trees are calculated on either the complete alignment, or just the -currently selected group of sequences. 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. -

The Tree Viewing Window

- When the tree has been calculated a window is displayed showing the - tree, with the leaves labelled with sequence ids. -

Selecting the 'show distances' checkbox will put branch lengths on the branches. - These branch lengths are the percentage mismatch between two nodes.

- -

- Selecting sequence ids at the leaves of the tree selects sequences - in the original alignment. These selections are reflected in any - other analysis windows open on the same alignment.

- Clicking on an internal node of the tree will rearrange the tree - diagram, inverting the ordering of the branches at that node. -

- Clicking anywhere along the extent of the tree (but not on a leaf or - internal node) defines a tree 'partition', by cutting every branch - of the tree spanning the depth where the mouse-click occured. Groups - are created containing sequences at the leaves of each connected - subtree. These groups are each given a different colour, which are - reflected in other windows in the same way as if the sequence ids - were selected, and can be edited in the same way as user defined - sequence groups. -

Tree partitions are useful for comparing clusterings produced by -different methods and measures. They are also an effective way of -identifying specific patterns of conservation and mutation -corresponding to the overall phylogenetic structure, when combined -with the conservation -based colour scheme.

- - -

External Sources for Phylogenetic Tree Construction

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. See the - Phylogenetic Web - Services page for directly accessible methods. It will also be - possible to read trees into Jalview directly, in the near future. -

- - - + + + +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. +
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. +

+ + + +