GenGIS at iEvoBio 2012

GenGIS 2: Geospatial Analysis of

Genetic and Genomic Datasets

Donovan Parks

GenGIS 2: Geospatial Analysis of

Genetic and Genomic Datasets

Donovan Parks

Timothy Mankowski

Mike Porter

Brett O’Donnell

Rob Beiko

2 of 12http://kiwi.cs.dal.ca/GenGIS

software for biogeography


applicable to many datasets

General-purpose environment for visualizing and

analyzing molecular data in a spatial context

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Distribution of ssDNA phages

Biogeography of

Kangaroo apples Geographic spread of Influenza A

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al., B

JL

S, 2

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Phylogeography of Patagonian fish


site-by-site summary statistics

Visualizations:

Pie charts

Bar charts

Features:

Filtering

Colour maps

Distribution of H1V-1 subtypes in

Africa

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om

e R

es,

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Data

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, 2

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Biogeography of bacterial

communities on the human body


georeferenced trees

3D geophylogeny of E. eschscholtzii

salamanders

Top view of Ensatina

eschscholtzii

salamander geophylogeny

2D geotree indicating similarity of

marine microbial communities

Parks et al., Genome

Res, 2009Parks and Beiko, Geoinformatics,

2009


testing linear gradients

Phylogeography of Banza katydids in Hawaii

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Be

iko, G

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info

rmatics, 2

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Optimize layout of tree to minimize ‘crossings’ with

respect to a geographic axis


linear axes analysis

Evaluate all linear

geographic axes

Parks et al., in preparation


non-linear gradients

Migration of Ensatina eschscholtzii salamanders from the western United

States

Parks and

Beiko, Geoinformatics, 2009

Linear gradient - 37 crossings Non-linear gradient - 11 crossings


statistical tests

Linear regression, Mantel test, others via R

Regression of species richness and

latitude

Interface for performing linear

regression and generating

visualizations

Parks et al., in preparation


dissimilarity-matrix visualizer

Visualize:

Beta diversity

Rates of gene flow

Viral transmission rates

Rate of HIV-1

exported from Spain

to surrounding

countries

Data

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m P

ara

ske

vis

et

al., R

etr

oviro

logy,

20

09

Thirteen countries in Africa with a H1V-1

subtype distribution most similar to

Tanzania


customizable

Perform custom analyses

GenGIS API accessible via Python console

All data in GenGIS exposed in API

R statistical language accessible via RPy2

Create plugins with graphical interfaces

Using Python and wxPython

e.g., Linear regression, Mantel test

Create custom visualizations

e.g., Dissimilarity-matrix visualizer

Brought to you by…

Rob Beiko ([email protected])

Mike Porter

Timothy Mankowski

Brett O’Donnell

Suwen Wang

Sylvia Churcher

Christian Blouin

Jacqueline Whalley

Stephen Brooks

Find us at the Software

Bazaar!

http://kiwi.cs.dal.ca/GenGIS

Phylogeography of Banza katydids in Hawaii

GenGIS at iEvoBio 2012

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