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 :

• PID
  The percentage identity between the two sequences at each aligned position.
• 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.

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.