Tree Calculation

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Ftree.html;h=59736ca8793dc5304a990b37248a8c080798434c;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=0e9ba3efd6ca2e3ce68b4254fc3618da620612fd;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html index 0e9ba3e..59736ca 100755 --- a/help/html/calculations/tree.html +++ b/help/html/calculations/tree.html @@ -1,83 +1,128 @@ -Tree Calculation + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> + +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
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.

+ 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.