Dendroscope An interactive viewer for large phylogenetic trees

1
Dendroscope An interactive viewer for large
phylogenetic trees
- and networks

• Daniel H. Huson

Phylogenetics Programme, Newton Institute,
September 2007
2
Overview

• Dendroscope and large trees
• Phylogenetic networks
• cluster networks
• Dendroscope 2 and phylogenetic networks

3
Yet Another Tree Viewer?

• http//evolution.genetics.washington.edu/phylip/so
  ftware.html
• Yet no existing program does it all

4
Requirements

• Provide all standard visualizations
• Allow interactive setting of line widths, colors
  and fonts
• Allow rerooting, reordering, hiding, deletion and
  subtree extraction
• Open and save in different formats, including
  standard graphics formats
• Run on large files with many trees or large trees
  (with a million nodes)
• Run on all major operating systems

5
Eight Different Views
6
Multiple Trees
List of trees can be loaded and edited
7
Large Trees
NCBI taxonomy 325,000 taxa
8
Finding Taxa in Large Trees
9
Subtree Extraction
Select a set of taxa and extract the
induced subtree
10
Overview

• Dendroscope and large trees
• Phylogenetic networks
• cluster networks
• Dendroscope 2 and phylogenetic networks

11
The Splits of a Tree

• Every edge of a tree defines a split of the taxon
  set X

e
x1,x3,x4,x6,x7 vs x2,x5,x8
12
Trees and Compatible Splits

• The set of all splits obtained from T is called
  the split encoding ?(T) of T
• Theorem
• An arbitrary set of splits ? is the split
  encoding of some unique unique tree T, if and
  only if any two splits in ? are compatible.
• How to represent incompatible splits?

13
Split Networks

• Display incompatible splits using
  bands of parallel edges
• (Bandelt Dress, 1992)
• Boxes artifacts of this,
  non-intuitive for users?
• Size of network can be exponential in
  of splits
• Only drawn in unrooted radial layout
• Different from reticulate networks
• Find a new way to represent incompatible splits?

14
Hasse Diagram

• Stefan Gruenewald (MPI Shanghai) why not use a
  Hasse diagram or cover digraph?
• Because clusters then represented by nodes, not
  edges

A,B,C,D,E
Clusters (rooted splits) A B C D
E A,B B,C D,E C,D,E A,B,C,D,E
C,D,E
A,B
B,C
D,E
A
B
C
D
E
15
Idea Extend the Hasse Diagram

• Represent every cluster by its in-edge

A,B,C,D,E
C,D,E
A,B
B,C
D,E
A
B
C
D
E
?
16
Idea Extend the Hasse Diagram

• If in-degree gt1, insert new edge

A,B,C,D,E
C,D,E
A,B
B,C
D,E
A
B
D
E
C
17
Cluster Network

• A new type of network?

A,B,C,D,E
C,D,E
A,B
B,C
D,E
A
D
E
B
C
18
Split Network vs Cluster Network
Split network
Cluster network
Data (Kumar, 1998)
19
Cluster Network vs Reticulate Network

• Cluster network Hard-wired blue edges always
  on
• Canonical network, computationally easy
• Reticulate net. Soft-wired For any split, any
  blue edge can be on or off
• Minimum reticulate network, computationally hard

20
Overview

• Dendroscope and large trees
• Phylogenetic networks
• cluster networks
• Dendroscope 2 and phylogenetic networks

21
Dendroscope 2

• Computation of different consensus trees and
  super trees
• Computation of different consensus networks and
  super networks
• Use extended Newick format to support cluster
  networks and reticulate networks
• All features of Dendroscope 1 will also apply to
  networks

22
Example Five Fungal Trees
Five fungal trees (Pryor 2000, 2003) ITS (two
trees) SSU (two trees) Gpd (one tree) Number of
taxa 29-46, total is 63
23
Strict Consensus Tree
24
Majority Consensus Tree
25
Consensus Super Network, gt20 support
26
Super Network, All Splits
27
Summary

• Dendroscope 1 new interactive tool for
  visualizing editing phylogenetic trees
• Cluster networks new type of phylogenetic
  networks that are easy to compute and look more
  like trees
• Dendroscope 2 will contain consensus methods and
  will read, write and draw cluster- and reticulate
  networks.
• Dendroscope 1 is freely available from

www-ab.informatik.uni-tuebingen.de/software.dendro
scope
28
Credits

• Contributions to Dendroscope from
• Tobias Dezulian, Markus Franz, Christian Rausch,
  Daniel Richter Regula Rupp
• Super network algorithm (Z-closure) joint work
  with
• Tobias Dezulian, Tobias Klöpper and Mike
  Steel
• Filtered super network joint work with
• Mike Steel and Jim Whitfield