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 : -
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. -
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. -
- - - + + +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 : +
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. +
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. +
+ + + +