Bayesian Phylogenetic Infererence: Evaluate MrBayes Run

Created: 2013-02-20 13:42:45 Last updated: 2015-06-12 13:39:21

Download Workflow

Retrieve Phylogenetic inference with MrBayes and test of MCMC convergence (GEOKS) and fit of the model on the data (Posterior Predictive test)

Preview

Download as scalable diagram (SVG)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://myexperiment.org/workflows/3407/download?version=3
[ More Info Expand ]

Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (2)

Name	Description
JobID
NexusFileName

Processors (31)

Name	Type	Description
Call_Retrieve_MrBayesJob	workflow
Call_Retrieve_GeoKS_Job	workflow
Concatenate_three_strings	localworker	Script output = Mode+' '+ Alpha+' '+Path;
Ask_ConvergenceMode	stringconstant	Value convergence
Ask_GeoKS_Service	stringconstant	Value geoks_xml
ShowWebPage	workflow
Split_string_into_string_list_by_regular_expression_erase_last	localworker	Script List split = new ArrayList(); if (!string.equals("")) { String regexString = ","; if (regex != void) { regexString = regex; } String[] result = string.split(regexString); for (int i = 0; i < (result.length-1); i++) { split.add(result[i]); } }
String_constant_2_2_2	stringconstant	Value /
DownloadMRBayesOutput	workflow
FileAddress_Spacer	stringconstant	Value /
Split_string_into_string_list_by_regular_expression_erase_last_2	localworker	Script List split = new ArrayList(); if (!string.equals("")) { String regexString = ","; if (regex != void) { regexString = regex; } String[] result = string.split(regexString); for (int i = 0; i < (result.length-1); i++) { split.add(result[i]); } }
Merge_String_List_to_a_String	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();
Merge_String_List_to_a_String_2	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();
ask_AlphaXGeoKS	interaction	Interaction Page ask
Ask_Alpha	stringconstant	Value Choose the minimal probability value that the observed MCMC integration has converged (e.g. 0.1, 0.95)
Call_Retrieve_ConsensusTree	workflow
Workflow31	workflow
Parsing_GeoKS	workflow
Concatenate_two_strings	localworker	Script PartArgument = " " +Burnin;
Concatenate_two_strings_2	localworker	Script output = string1 + string2;
XPath_Service	xpath	Xpath Expression res/tree
PosterioPredictiveTest	workflow
MrBayesPPtest	stringconstant	Value MrBayesPPtest
Concatenate_Four_strings	localworker	Script output = nameRun + ' ' +pathInputMrBayes + ' ' +numberSample + ' '+burninvalue;
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); }
Workflow20	workflow
Workflow20_2	workflow
MakeHistogram	workflow
ask_PPTSize	interaction	Interaction Page ask
message_value	stringconstant	Value Sample Size from the Posterior Distribution to test fit of model on Data
Text_constant	stringconstant	Value 0.05

Beanshells (1)

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

Outputs (6)

Name	Description
URL_Output_file	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
GeoKS_Result	Restul of the GeoKS test of convergence.
convergence	path to obtain the output file of program geoks
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
xmlTest	Result of the Posterior Predictive test. the XML gives the details of the bolback test and the different component of the ibrahim statistics
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.

Datalinks (42)

Source	Sink
JobID	Call_Retrieve_MrBayesJob:jobID
Concatenate_three_strings:output	Call_Retrieve_GeoKS_Job:Argument
Ask_GeoKS_Service:value	Call_Retrieve_GeoKS_Job:Name
Call_Retrieve_MrBayesJob:Output_Path	Concatenate_three_strings:Path
Ask_ConvergenceMode:value	Concatenate_three_strings:Mode
ask_AlphaXGeoKS:answer	Concatenate_three_strings:Alpha
Merge_String_List_to_a_String:concatenated	ShowWebPage:URL
Call_Retrieve_MrBayesJob:Output_Path	Split_string_into_string_list_by_regular_expression_erase_last:string
String_constant_2_2_2:value	Split_string_into_string_list_by_regular_expression_erase_last:regex
Merge_String_List_to_a_String_2:concatenated	DownloadMRBayesOutput:URL
FileAddress_Spacer:value	Split_string_into_string_list_by_regular_expression_erase_last_2:regex
Call_Retrieve_GeoKS_Job:Output_Path	Split_string_into_string_list_by_regular_expression_erase_last_2:string
Split_string_into_string_list_by_regular_expression_erase_last:split	Merge_String_List_to_a_String:stringlist
String_constant_2_2_2:value	Merge_String_List_to_a_String:seperator
Split_string_into_string_list_by_regular_expression_erase_last_2:split	Merge_String_List_to_a_String_2:stringlist
FileAddress_Spacer:value	Merge_String_List_to_a_String_2:seperator
Ask_Alpha:value	ask_AlphaXGeoKS:message
Concatenate_two_strings_2:output	Call_Retrieve_ConsensusTree:Argument
XPath_Service:nodelist	Workflow31:NewickString
Call_Retrieve_GeoKS_Job:GeoKS_Result	Parsing_GeoKS:GeoKS_XML
Parsing_GeoKS:Burnin	Concatenate_two_strings:Burnin
Concatenate_two_strings:PartArgument	Concatenate_two_strings_2:string2
Call_Retrieve_MrBayesJob:Output_Path	Concatenate_two_strings_2:string1
Call_Retrieve_ConsensusTree:NewickTrees	XPath_Service:xml_text
MrBayesPPtest:value	PosterioPredictiveTest:Name
Concatenate_Four_strings:output	PosterioPredictiveTest:Argument
Call_Retrieve_MrBayesJob:Output_Path	Concatenate_Four_strings:pathInputMrBayes
Parsing_GeoKS:Burnin	Concatenate_Four_strings:burninvalue
ask_PPTSize:answer	Concatenate_Four_strings:numberSample
NexusFileName	Concatenate_Four_strings:nameRun
Parsing_GeoKS:Success	condition_checker:condition
condition_checker:pass_flags	Workflow20:Sentinel
condition_checker:fail_flags	Workflow20_2:Sentinel
PosterioPredictiveTest:XML_Report	MakeHistogram:XML
Text_constant:value	MakeHistogram:Alpha
message_value:value	ask_PPTSize:message
Call_Retrieve_ConsensusTree:Output_Path	URL_Output_file
Call_Retrieve_GeoKS_Job:GeoKS_Result	GeoKS_Result
Call_Retrieve_GeoKS_Job:Output_Path	convergence
Call_Retrieve_ConsensusTree:NewickTrees	newickTree
PosterioPredictiveTest:XML_Report	xmlTest
MakeHistogram:plot	Plot