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Dendroscope – An interactive viewer for large phylogenetic trees

Dendroscope – An interactive viewer for large phylogenetic trees. - and networks. Daniel H. Huson. Phylogenetics Programme, Newton Institute, September 2007. Overview. Dendroscope and large trees Phylogenetic networks cluster networks Dendroscope 2 and phylogenetic networks.

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Dendroscope – An interactive viewer for large phylogenetic trees

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  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

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