BEAST2 workflow. Jūlija Pečerska & Veronika Bošková
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1 BEAST2 workflow Jūlija Pečerska & Veronika Bošková
2 Tools needed
3 Tools needed BEAST2: Software implementing MCMC for model parameter and tree inference
4 Tools needed BEAST2: Software implementing MCMC for model parameter and tree inference BEAUti: Part of the BEAST2 package, GUI for setting up the input file
5 Tools needed BEAST2: Software implementing MCMC for model parameter and tree inference BEAUti: Part of the BEAST2 package, GUI for setting up the input file Tracer: Tool for summarising BEAST2 output files (.log)
6 Tools needed BEAST2: Software implementing MCMC for model parameter and tree inference BEAUti: Part of the BEAST2 package, GUI for setting up the input file Tracer: Tool for summarising BEAST2 output files (.log) Tree Annotator: Tool for summarising BEAST2 output files (.trees)
7 Tools needed BEAST2: Software implementing MCMC for model parameter and tree inference BEAUti: Part of the BEAST2 package, GUI for setting up the input file Tracer: Tool for summarising BEAST2 output files (.log) Tree Annotator: Tool for summarising BEAST2 output files (.trees) FigTree/IcyTree/DensiTree: Tools for visualisation of trees (.trees)
8 Tools needed BEAST2: Software implementing MCMC for model parameter and tree inference BEAUti: Part of the BEAST2 package, GUI for setting up the input file Tracer: Tool for summarising BEAST2 output files (.log) Tree Annotator: Tool for summarising BEAST2 output files (.trees) FigTree/IcyTree/DensiTree: Tools for visualisation of trees (.trees) R(+RStudio)/Python/Matlab/etc: Post analysis, plotting, etc.
9 Workflow ACACACCC TCACACCT ACAGACTT
10 Workflow ACACACCC TCACACCT ACAGACTT BEAUti
11 Workflow ACACACCC TCACACCT ACAGACTT BEAUti xml file BEAST2
12 Workflow ACACACCC TCACACCT ACAGACTT Tracer log file BEAUti xml file BEAST2
13 Workflow ACACACCC TCACACCT ACAGACTT Tracer TreeAnnotator log file trees file BEAUti xml file BEAST2
14 BEAUti Bayesian Evolutionary Analysis Utility GUI for setting up BEAST2 input file in xml format. Input: Sequence alignment! Output: XML file
15 BEAUti Bayesian Evolutionary Analysis Utility GUI for setting up BEAST2 input file in xml format. Input: Sequence alignment! Output: XML file
16 BEAUti Bayesian Evolutionary Analysis Utility GUI for setting up BEAST2 input file in xml format. Input: Sequence alignment! Output: XML file
17 BEAUti Bayesian Evolutionary Analysis Utility GUI for setting up BEAST2 input file in xml format. Input: Sequence alignment! Output: XML file
18 BEAST2 Bayesian evolutionary analysis by sampling trees 2 Performs MCMC analyses of sequences under selected sequence evolution and tree model; Planned as an extension of BEAST1, but now a separate package; Has a modular design that makes it easy to extend. Input: XML file Output: log file trees file
19 BEAST2 BEAST 2.1 BEAST 1.8 COALESCENT TREE PRIORS! Constant size Drummond 2002 Drummond 2002 Exponential growth Drummond 2002 Drummond 2002 Bayesian skyline Drummond 2005 Drummond 2005 Extended Bayesian skyline Heled 2008 Heled 2008 Bayesian skygrid X Gill 2013 Deterministic closed SIR In preparation Dearlove 2013 BIRTH-DEATH TREE PRIORS Yule Yule with one calibration Heled 2012 Birth-death Calibrated birth-death Heled 2013 X Birth-death with incomplete sampling X Birth-death serial sampling Stadler 2012 X Birth-death serial skyline Stadler 2013 X Birth-death SIR Kuhnert 2013 X AND MORE
20 BEAST2
21 BEAUti installing BEAST2 packages! In BEAUti: File > Manage Packages
22 BEAUti installing BEAST2 packages! In BEAUti: File > Manage Packages
23 Tracer Summarises log files from BEAST2 runs;! Allows to check mixing, ESS, parameter correlations;! Gives an overview of posterior parameter estimates;! Lets one compare results of several analyses. Input: log file Output: insight
24 Tracer
25 ` Tracer
26 Tracer ` Mixing well!
27 Tracer ` Mixing well! Not mixing!
28 TreeAnnotator Analyse trees file from BEAST2 runs;! Produces Maximum Clade Credibility (MCC tree) with node annotations (posterior probability); Input: trees file Output: summary (MCC) tree 8
29 TreeAnnotator 8
30 FigTree View tree sets and summary trees from BEAST2 runs. Input: trees file Output: insight
31 FigTree
32 FigTree
33 DensiTree View the distribution of trees from BEAST2 runs. Input: trees file Output: insight
34 DensiTree
35 Time to tame!
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