From 8ee7a0f79f6da26d5011c60a80226d6994733cab Mon Sep 17 00:00:00 2001
From: jprocter
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.
+A newly calculated tree will be displayed in a new tree viewing window. In +addition, a new entry with the same treeviewer 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.
- -External Sources for Phylogenetic Tree Construction
+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. 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. + 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
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