Slides for my lightning talk on the SUPERSMART platform to the SSB/SSE/ASN annual meeting, Austin, TX, USA. SSB Spotlight Session: "Next generation phylogenetic inference 2". Monday, June 20th 2016, 3:20PM, Ballroom A.
Self-Updating Platform for the Estimation of Rates of Speciation, Migration And Relationships of Taxa: SUPERSMART
1.
h#p://www.supersmart-‐project.org
Self-‐Updating
Platform
for
the
Estimation
of
Rates
of
Speciation,
Migration,
And
Relationships
of
Taxa
Rutger
Vos,
Naturalis
Biodiversity
Center,
Leiden,
the
Netherlands
@rvosa
5. Effect
of
data
mining
parameterization
h#p://www.supersmart-‐project.org
-‐
@rvosa
0 5 10 15 20
0.050.100.150.20
Averaged posterior probabilities on nodes
Minimum marker coverage per taxon
Maximumaverageduncorrectedpairwisedistance
p
<
0.8
0.8
<
p
<
0.95
p
>
0.95
6. Recovering
a
simulated
tree
Simulated
Tree
Re-estimated
Tree
data sim
0.000.10
data sim
60708090
% of invariant sites
per alignment
%
data sim
0102030
Number of indels
per alignment
count
data sim
04080120
data sim
0200400
data sim
02040
average distance
within alignment
relativeeditdistance
Average size of indels
per alignment
size(nucleotides)
Number of gaps
per sequence
gapcount
% gaps per sequence
%
!" #"
time
(myr)
80 0 0 80
h#p://www.supersmart-‐project.org
-‐
@rvosa
7. Install
a
vagrant
box,
then:
$
smrt [COMMAND] [OPTIONS]
h#p://www.supersmart-‐project.org
-‐
@rvosa
8. Acknowledgements
h#p://www.supersmart-‐project.org
-‐
@rvosa
The
smar,es:
• Alexandre
Antonelli
• Rutger
Vos
• Hannes
He#ling
• Mike
Sanderson
• Bengt
Oxelman
• Karin
Nilsson
• Mats
Töpel
• Hervé
Sauquet
• Henrik
Nilsson
• Daniele
Silvestro
• Fabien
Condamine
• Ruud
Scharn
Thank
you
to:
• Erick
Matsen
• Meg
Pirrung
• You,
the
audience!