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Dendroscope –Dendroscope –An interactive viewer for An interactive viewer for large phylogenetic treeslarge phylogenetic trees

Daniel H. Huson

Phylogenetics Programme, Newton Institute, September 2007

- and networks- and networks

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OverviewOverview

Dendroscope and large trees

Phylogenetic networks– cluster networks

Dendroscope 2 and phylogenetic networks

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Yet Another Tree Viewer?Yet Another Tree Viewer? http://

evolution.genetics.washington.edu/phylip/software.html:

Yet… no existing program “does it all”

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RequirementsRequirements 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

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Eight Different ViewsEight Different Views

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Multiple TreesMultiple Trees

List of treescan be loadedand edited

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Large TreesLarge Trees

NCBItaxonomy~325,000taxa

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Finding Taxa in Large TreesFinding Taxa in Large Trees

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Subtree ExtractionSubtree Extraction

Select a set of taxaand extractthe inducedsubtree

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OverviewOverview

Dendroscope and large trees

Phylogenetic networks– cluster networks

Dendroscope 2 and phylogenetic networks

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x1

x8

x7

x6

x5

x4

x3

x2

x8

x5

x2

The Splits of a TreeThe Splits of a Tree Every edge of a tree defines a split

of the taxon set X:

x1,x3,x4,x6,x7 vs x2,x5,x8

e

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Trees and Compatible SplitsTrees 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?

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Split NetworksSplit 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?

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Hasse DiagramHasse Diagram Stefan Gruenewald (MPI Shanghai): why not use a

“Hasse diagram” or “cover digraph”?

Because clusters then represented by nodes, not edges

Clusters (“rooted splits”):{A} {B} {C} {D} {E}{A,B} {B,C} {D,E}{C,D,E}{A,B,C,D,E}

{A,B,C,D,E}

{C,D,E}

{A,B} {B,C} {D,E}

{A} {B} {C} {D} {E}

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Idea: Extend the Hasse DiagramIdea: 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}

?

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Idea: Extend the Hasse DiagramIdea: 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} {D} {E}{C}

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““Cluster Network”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}

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Split Network vs Cluster NetworkSplit Network vs Cluster Network

Data: (Kumar, 1998)

Split network Cluster network

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Cluster Network vs Reticulate Cluster Network vs Reticulate NetworkNetwork

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

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OverviewOverview

Dendroscope and large trees

Phylogenetic networks– cluster networks

Dendroscope 2 and phylogenetic networks

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Dendroscope 2Dendroscope 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

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Five fungal trees Five fungal trees (Pryor 2000, 2003):(Pryor 2000, 2003):

ITS (two trees)ITS (two trees)SSU (two SSU (two trees)trees)Gpd (one tree)Gpd (one tree)

Number of taxa:Number of taxa:29-46, total is 6329-46, total is 63

Example: Five Fungal TreesExample: Five Fungal Trees

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““Strict Consensus Tree”Strict Consensus Tree”

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““Majority Consensus Tree”Majority Consensus Tree”

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Consensus Super Network, >20% Consensus Super Network, >20% supportsupport

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Super Network, All SplitsSuper Network, All Splits

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SummarySummary 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

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CreditsCredits 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