BEAST 2 BEAST 2 RB subst model BEAST Add-Ons Remco R. Bouckaert - - PowerPoint PPT Presentation

BEAST 2 Remco Bouckaert BEAST 2 RB subst model BEAST Add-Ons

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BEAST 2

Remco R. Bouckaert remco@cs.{auckland|waikato}.ac.nz rrb@xm.co.nz Department of Computer Science University of Auckland & University of Waikato

BEAST 2 Remco Bouckaert BEAST 2 RB subst model BEAST Add-Ons

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What BEAST 2 does

• The kind of Bayesian analysis as per citations on the

BEAST 1 wiki

• BEAUti 2: GUI to specify analysis
• Sequence generator for simulation studies
• Some post processing tools: log analyser, log

combiner, DensiTree

• Documentation for all the above – from user to

developer, XML tweaker, etc.

BEAST 2 Remco Bouckaert BEAST 2 RB subst model BEAST Add-Ons

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What BEAST 2 does that BEAST 1 doesn’t... ...hence why you want to use BEAST 2

• Can resume runs when a chain is not mixing well
• BEAUti 2: reload existing specifications – reduced

need for XML hacking

• Logs model with trace – allows looking up where the

trace comes from

• Provide a platform to develop add-ons - powerful

interface, easy extensible XML, templates for BEAUti.

• Book pending – expected 2012

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BEAST Add-Ons Consider BEAST 2 as a library for MCMC and phylogenetics A BEAST 2 add-on is a library based on BEAST 2 Why add-ons:

• Making work easier citable
• Making the core easier to learn – it’s a lot smaller /

cleaner

• Separating out stable / experimental code / dead

code

• ...

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Add-ons

• SnAPP - multi-species coalescent for SNP and AFLP

data http://snapp.otago.ac.nz/

• beastii - utilities, parallel treelikelihood, spreadsheet

http://code.google.com/p/beastii/

• BDSKY: birth death skyline – handles serially

sampled tips http://code.google.com/p/bdssm-beast2/

• Subst-BMA - Bayes model averaging over subst.

models http://code.google.com/p/subst-bma/

• Beast classic http://code.google.com/p/beast-classic
• Phylogeography http://code.google.com/p/beast-geo
• Protein evolution http://code.google.com/p/evoprotein
• Demographic model http://code.google.com/p/coalsir
• Graphics http://code.google.com/p/beast-graphics/
• RB-substitution model? ...

BEAST 2 Remco Bouckaert BEAST 2 RB subst model BEAST Add-Ons

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Reversible-jump Based (RB) substitution model for nucleotides A

α β γ

• G

δ

• ω

C

ǫ

T R =

• α

β γ α

• δ

ǫ β δ

• ω

γ ǫ ω

• frequencies π

Q = πR transition prob. P(t) = eQt Hierarchy of models α β γ δ ǫ ω # dimensions F81 (JC69) 1 1 1 1 1 1 HKY85 (K80) a 1 a a 1 a 1 TN93 a b a a 1 a 2 TIM a b c c 1 a 3 new a b c d 1 a 4 GTR (SYM) a b c d 1 e 5 Increase dimension by drawing a new parameter value from Γ(0.2, 5)

BEAST 2 Remco Bouckaert BEAST 2 RB subst model BEAST Add-Ons

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Drawing from Prior Exponential (mean 1) prior on parameters

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Simulating from subst model

6 taxa, 3000 sites, tree from ape data, Yule tree prior, no gamma, 0 prop

BEAST 2 Remco Bouckaert BEAST 2 RB subst model BEAST Add-Ons

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Hepatitis C: HKY massively preferred (None of the dataset fits F81/JC69)

44 taxa, 576 sites, Bayesian skyline, 0 gamma, 0 prop invariant

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Apes: HKY preferred, but higher order models are explored as well

6 taxa, 768 sites, Yule treeprior, 0 gamma, 0 prop invariant same pattern for Darwin finches, Bird flu

BEAST 2 Remco Bouckaert BEAST 2 RB subst model BEAST Add-Ons

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Gophers: TN93 preferred, but HKY as well A

α β γ

• G

δ

• ω

C

ǫ

T

α β γ δ ω mean rate 0.181 0.525 0.143 0.094 0.200 ’old value’ 1 1 0.181 0.143 0.181

26 taxa, 614 sites, Yule treeprior, 0 gamma, 0 prop invariant

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Dengue virus: TN93 preferred (None of the dataset fits TIM or ’new’)

17 taxa, 1485 sites, Yule treeprior, 0 gamma, 0 prop invariant

BEAST 2 Remco Bouckaert BEAST 2 RB subst model BEAST Add-Ons

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HIV: only GTR will do

46 taxa, 2382 sites, Coalescent (exp), 0 Γ, 0 PI. MP , FPV, animal dna, primates.

Same results without and with partitioning sites at codon positions {1,2},{3} or {1},{2},{3}

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Effective sample size for all logged statistics for Ape (HKY), HVC (HKY), Dengue (TN93), Primates (GTR) In summary: RB subst models don’t require model selection, at no significant computational cost, and generate interpretable rates.

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RB Add-On: Implementing Plug-ins Everything is a Plug-in Plug-ins connect with other Plug-ins through Inputs Plug-ins and Inputs provide documentation, type checking, XML file parsing/producing

BEAST 2 Remco Bouckaert BEAST 2 RB subst model BEAST Add-Ons

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Creating a new RB subst model add-on

• Check out BEAST 2 from google code.
• Create a project in your favorite IDE (Eclipse, Intellij,

etc) with a dependency on BEAST2 and do some programming...

• Create documentation (examples, README, etc.)
• Create BEAUti template (optional)
• Wrap in a zip file and publish through beast2 wiki

http://beast2.cs.auckland.ac.nz/

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Installing RB subst model add-on

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Installing RB subst model add-on

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Why create BEAST add-ons

• No need to program an MCMC framework or

phylogenetics library, file IO, etc.

• Requires little effort to add to GUI
• Easy way to distribute new models to users

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Summary

• BEAST 2 is ready to be used, most standard models

from BEAST 1 are available

• BEAST 2 has some models not in BEAST 1, like

SNAPP and RB subst model

• (The RB substitution model appears to select models

at no extra computational cost)

• Writing BEAST add-ons is (relatively) easy
• Let me know if you need help setting up your own

add-on