Post on 07-Jul-2015
description
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
3 of 12http://kiwi.cs.dal.ca/GenGIS
applicable to many datasets
General-purpose environment for visualizing and
analyzing molecular data in a spatial context
Pa
rks e
t a
l., P
Lo
S C
urr
,
20
09P
ocza
i e
t a
l., M
ol B
iolR
ep
,
20
09
Tu
cke
r e
t a
l.,
ISM
E J
,
20
10
Distribution of ssDNA phages
Biogeography of
Kangaroo apples Geographic spread of Influenza A
Ruzza
nte
et
al., B
JL
S, 2
011
Phylogeography of Patagonian fish
4 of 12http://kiwi.cs.dal.ca/GenGIS
site-by-site summary statistics
Visualizations:
Pie charts
Bar charts
Features:
Filtering
Colour maps
Distribution of H1V-1 subtypes in
Africa
Pa
rks e
t a
l., G
en
om
e R
es,
20
09
Data
fro
m C
oste
llo e
t a
l., S
cie
nce
, 2
00
9
Biogeography of bacterial
communities on the human body
5 of 12http://kiwi.cs.dal.ca/GenGIS
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
6 of 12http://kiwi.cs.dal.ca/GenGIS
testing linear gradients
Phylogeography of Banza katydids in Hawaii
Pa
rks a
nd
Be
iko, G
eo
info
rmatics, 2
00
9
Optimize layout of tree to minimize ‘crossings’ with
respect to a geographic axis
7 of 12http://kiwi.cs.dal.ca/GenGIS
linear axes analysis
Evaluate all linear
geographic axes
Parks et al., in preparation
8 of 12http://kiwi.cs.dal.ca/GenGIS
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
9 of 12http://kiwi.cs.dal.ca/GenGIS
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
10 of 12http://kiwi.cs.dal.ca/GenGIS
dissimilarity-matrix visualizer
Visualize:
Beta diversity
Rates of gene flow
Viral transmission rates
Rate of HIV-1
exported from Spain
to surrounding
countries
Data
fro
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
11 of 12http://kiwi.cs.dal.ca/GenGIS
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 (beiko@cs.dal.ca)
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