Tree Calculation

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fcalculations%2Ftree.html;fp=help%2Fhtml%2Fcalculations%2Ftree.html;h=e18e273bc6e63d17a8266460e4a4915b193850f3;hb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;hp=1f3eecbb13213eec90b871bef20893f7e69f4d7e;hpb=247b4f59aad27b654fb55268b55645dc6496f12e;p=jalview.git diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html index 1f3eecb..e18e273 100755 --- a/help/html/calculations/tree.html +++ b/help/html/calculations/tree.html @@ -15,71 +15,4 @@ * PURPOSE. See the GNU General Public License for more details. * * 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.

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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. -

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