Tree Calculation

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Ftree.html;h=95904b6a18aa960e46a1c430fbe063c3ff7764bf;hb=001d029b058432b3ae0a4431e5bcd4116ee7694a;hp=b532aa3aa4c771e69d461c0ff471ef2595314443;hpb=1dff84dcfc6852d1010626c583a0b5c5f915c7ae;p=jalview.git diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html index b532aa3..95904b6 100755 --- a/help/html/calculations/tree.html +++ b/help/html/calculations/tree.html @@ -19,82 +19,110 @@ * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. --> -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.

+ 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. +
- 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 the normalised - hamming distance between the sequence features observed in each column of - the alignment.

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.

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. +

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.

+ 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. +

+ 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.