Select Model For Me with components

Created: 2013-02-20 12:55:59 Last updated: 2014-01-31 11:28:33

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Phylogenetic inference with MrBayes. The the model of evolution is defined with the help of PartitionFinder, inference and test of MCMC convergence (GEOKS) and fit of the model on the data (Posterior Predictive test)

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (8)

Name	Description
MSA_fasta	Multiple Sequence Alignment in Fasta format
Possible_Partition	Partitioning of the MSA using nexus/raxml syntax. Define at least 2 partitions. Partition could define codon positions and/or gene boundaries and/or domains
Statistical_Criterium	What statistical criterium should be used to compare different models? AIC = Aikake information Criterium AICc =Aikake information Criterium correct per sample size BIC = Bayesian Information Criterium 3 possible values: AIC, AICc, or BIC
Number_of_runs	Number of independent runs to check convergence of the markovian integration necessary to perform bayesian phylogenetic inference. Minimum value 2. Always an integer
Number_of_MCMCMC_generations	Number of Generation for each run of the markovian integration necessary to the phylogenetic inference. The convergence test (GeoKS) will tell post hoc if the number was sufficient. If is not the case try with a larger number following the educated guess of GeoKS
File_name	Filename for nexus input file
Linking_branches	Should models assume that branches in the tree are linked or unlinked across alignment parts? Two possible strings: linked unlinked
SampleSize	Sample Size from the Posterior Distribution to test fit of model on Data. This integer should be smaller than number of generation divided by 100.

Processors (14)

Name	Type	Description
SelectingEvolutionaryModelWithPartFinder	component	http://www.myexperiment.org/workflows/3943.html Component SelectingEvolutionaryModelWithPartFinder
MrBayes	component	Component MrBayes
JSTWebDav3Input	component	http://www.myexperiment.org/workflows/3942.html Component JSTWebDav3Input
RandGen	localworker	Script import java.util.Random; Random r = new Random(); Integer a=r.nextInt(); if (a<0){ a=-1*a; } out=a ;
ConVergenceTreeDiagnosticGeoKS	component	http://www.myexperiment.org/workflows/3945.html Component ConVergenceTreeDiagnosticGeoKS
condition_checker	beanshell	This service checks if the condition is "true" and if so outputs a value in the pass_flags list and leaves the fail_flags empty. If the condition is not true then the service outputs a value in the fail_flags list and leaves the pass_flags empty. Script import java.util.ArrayList; ArrayList pass_flags = new ArrayList(); ArrayList fail_flags = new ArrayList(); if (condition.equals("True")) { pass_flags.add(condition); } else { fail_flags.add(condition); }
Success_check	workflow
ConsensusTree	component	http://www.myexperiment.org/workflows/3946.html Component ConsensusTree
TreeVisualizationItol	component	http://www.myexperiment.org/workflows/3947.html Component TreeVisualizationItol
MrBayesPPtest	component	http://www.myexperiment.org/workflows/3952.html Component MrBayesPPtest
NoSpace	beanshell	Script out1=string.replaceAll(" ","_");
TargetOnly	beanshell	Script out1=string.replaceAll(".+/","");
Failure_check	workflow
String_List_Union	localworker	Script Set results = new HashSet(); results.addAll(list1); results.addAll(list2); List union = new ArrayList(); union.addAll(results);

Beanshells (3)

Name	Description	Inputs	Outputs
condition_checker	This service checks if the condition is "true" and if so outputs a value in the pass_flags list and leaves the fail_flags empty. If the condition is not true then the service outputs a value in the fail_flags list and leaves the pass_flags empty.	condition	pass_flags fail_flags
NoSpace		string	out1
TargetOnly		string	out1

Outputs (11)

Name	Description
Plot	Result of the Posterior Predictive test. Histogram of the distribution of the complexities (log of sum of sites entropy or maximal possible loglikelihood score) of the simulated data using the posterior distribution parameters compared with observed data complexity. The 1-alpha high posterior density of the distribution show the region where simulate data complexity match the observed one. Larger observed complexity indicates model too simplistic, while the contrary indicates overparametrization of the model.
newickTree	small xml with tag res with one or more tag tree each one with a body that contain a tree in netwick format. each tree represent the consensus for a given partition of group of partition in the same order that are cited in the nexus input file of mrbayes
Geoks	Result of the GeoKS test of convergence. XML format
PhyloInferenceOutput	The output of the consensus service is a path were to obtain a zipped folder that includes all output from phylogenetic inference and the one of the consensus
ViewTree	Link to visualize consensus Tree of phylogenetic inference. It could be more than one link if the model assume more than one tree (combination topology + branch length set). Use of the figure in the link below should be always accompagned by appropriate citation: Letunic I and Bork P (2011) Nucleic Acids Res doi: 10.1093/nar/gkr201 Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy
MrBayesOutput	original output of mrbayes
DetailsPPtest	Numeric Result of the Posterior Predictive test.
PartitionFinderOutput	Main output of PartitionFinder, where the preffered partitioned model is described
PartitionFinderDetails	Path were to retrieve all the detials of the partitionfinder software
GeoKSDetails	Path were to get all details of convergence test calculation.
log

Datalinks (41)

Source	Sink
Statistical_Criterium	SelectingEvolutionaryModelWithPartFinder:StatCriterium
Possible_Partition	SelectingEvolutionaryModelWithPartFinder:PossiblePartition
MSA_fasta	SelectingEvolutionaryModelWithPartFinder:MSA_fasta
Number_of_runs	SelectingEvolutionaryModelWithPartFinder:NumberRuns
Number_of_MCMCMC_generations	SelectingEvolutionaryModelWithPartFinder:MCMCMCGenerationNumber
Linking_branches	SelectingEvolutionaryModelWithPartFinder:LinkingBranches
RandGen:out	SelectingEvolutionaryModelWithPartFinder:Token
JSTWebDav3Input:REST_Service_redirection	MrBayes:Path2MrBayesInputFile
SelectingEvolutionaryModelWithPartFinder:MrBayesInput	JSTWebDav3Input:InputBody
RandGen:out	JSTWebDav3Input:Token
NoSpace:out1	JSTWebDav3Input:File_name
MrBayes:PathOfResultsFolder	ConVergenceTreeDiagnosticGeoKS:MrBayesOuputPath
ConVergenceTreeDiagnosticGeoKS:Success	condition_checker:condition
condition_checker:pass_flags	Success_check:Sentinel
MrBayes:PathOfResultsFolder	ConsensusTree:MrBayesFolder
ConVergenceTreeDiagnosticGeoKS:Burnin	ConsensusTree:BurnIn
ConsensusTree:Trees	TreeVisualizationItol:treefile
ConVergenceTreeDiagnosticGeoKS:Burnin	MrBayesPPtest:Burnin
SampleSize	MrBayesPPtest:SampleSize
MrBayes:PathOfResultsFolder	MrBayesPPtest:MrBayesOutputFolder
TargetOnly:out1	MrBayesPPtest:NameRun
File_name	NoSpace:string
JSTWebDav3Input:REST_Service_redirection	TargetOnly:string
condition_checker:fail_flags	Failure_check:Sentinel
TreeVisualizationItol:Log	String_List_Union:list2
MrBayesPPtest:Log	String_List_Union:list1
ConsensusTree:Log	String_List_Union:list1
ConVergenceTreeDiagnosticGeoKS:Log	String_List_Union:list1
SelectingEvolutionaryModelWithPartFinder:Log	String_List_Union:list1
MrBayes:Log	String_List_Union:list1
MrBayesPPtest:Plot	Plot
ConsensusTree:Trees	newickTree
ConVergenceTreeDiagnosticGeoKS:NiceXML	Geoks
ConsensusTree:ResultsFolder	PhyloInferenceOutput
TreeVisualizationItol:html	ViewTree
MrBayes:PathOfResultsFolder	MrBayesOutput
MrBayesPPtest:PPtestDetails	DetailsPPtest
SelectingEvolutionaryModelWithPartFinder:PartitionFinderOuput	PartitionFinderOutput
SelectingEvolutionaryModelWithPartFinder:Path	PartitionFinderDetails
ConVergenceTreeDiagnosticGeoKS:OutputPath	GeoKSDetails
String_List_Union:union	log