Tree Calculation

X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Ftree.html;h=e2629bc4e98345ce962e0ed00325e08468767fb2;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hb=c53aeee9a688f68d64106a968876e542f701fbc6;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5 diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html index e18e273..e2629bc 100755 --- a/help/html/calculations/tree.html +++ b/help/html/calculations/tree.html @@ -16,3 +16,70 @@ * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . --> +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.

+ +

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. +

+ + + +