1 / 28

Dendroscope 2: Interactive Tool for Phylogenetic Networks

Dendroscope 2 is an advanced tool for visualizing and editing phylogenetic trees and networks. It offers various features like rerooting, subtree extraction, and supports large trees with millions of nodes. The tool also allows for consensus tree and network computation, making it a comprehensive solution for phylogenetic analysis.

mcamp
Download Presentation

Dendroscope 2: Interactive Tool for Phylogenetic Networks

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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/software.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. x6 x4 x1 x8 x8 x5 x2 x5 x3 x7 x2 The Splits of a Tree • Every edge of a tree defines asplitof the taxon set X: e x1,x3,x4,x6,x7vsx2,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 >1, insert new edge: {A,B,C,D,E} {C,D,E} {A,B} {B,C} {D,E} {A} {B} {C} {D} {E}

  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, >20% 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.dendroscope

  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

More Related