visualing phylogenies: a personal view

Visualising phylogenies(a personal view)

@rdmpage

http://iphylo.blogspot.com

Trees suck…

http://vimeo.com/26210611

…in ways that maps don’t

Maps are predictable

Navigation is predictable

Every pixel counts

Ground truth

Relative and absolute navigation

Latitude 42.363921Longitude -71.087763

Phylogeny has none of this

There are few constraints on how we can draw trees

X

A

B

C

D

Y

X

B

A

D

C

Y

We can reorder Y

@broadinstitute

X

B

A

D

C

Y

X is a partial order

X

B

A

D

C

Y

X is a partial order

X: evolutionary distance

B

A

D

C

Y

X: time

B

A

D

C

Y

Y

X

Z?

What would third dimension represent?

@wellcometrust

Pretty, but…

Is 3D useful?

@systbiol

Y: la

titu

de

X:longitude

Z: evolutionary distance

@DavKidd @andrewxhill

@rdmpage

GenGIS2D geographically ordered tree

@rob_beiko

GenGIS-style trees on Google Maps

@rdmpage

Challenges

• Does 3D have a role beyond being a gimmick?

• Geospatial phylogenies

Big trees

11 June 2003

“best viewed when enlarged to a 1.5-meter diameter”

add

@rdmpage

@rdmpage

OneZoom

http://tree.opentree.org

Challenges

• A visualisation of large trees that is as intuitive and as useful as Google Maps

• A platform, not a picture

Touching the tree

@dr_pi

@kzelnio Think how great of a tool that could be at museumson a large flat screen at 4 year old height.

Dendroscope

Build-a-Treehttps://lifeonearth.seas.harvard.edu/learning-activities/bat/

Challenges

• Intuitive, easy to use touchable trees

• Teaching and research

• Gamefication

Where are the trees?

http://www.treebase.org/

58

0

1000

2000

3000

4000

5000

6000

7000

1975 1980 1985 1990 1995 2000 2005

Year

Cum

ula

tive n

um

ber

Rate of growth of phylogenetic knowledge

Number of papers with

“molecular” and

“phylogeny” in Web of

Science

Number of

studies in

TreeBASE

Why aren’t we archiving these trees?

http://dx.doi.org/10.1371/journal.pbio.1001636 (2013)

Challenges

• Interactive trees for publications and databases (eventually database = publication)

• Software to create pretty, machine readable visualisations

Tree challenges

Big trees Touch Accessibility