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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 (9)

Name	Description
MSA_fasta	Multiple Sequence Alignment in Fasta format
PossiblePartition	Partitioning of the MSA using nexus/raxml syntax
StatCriterium	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
NumberRuns	Number of indipendent runs to check convergence of the markovian integration necessary to perform bayesian phylogenetic inference. Minimum value 2. Always an integer
MCMCMCGenerations	Number of Generation for each run of the markovian integration necessary to the phylogenetic inference
Filename	Filename for nexus input file and prefix for all other input
LinkingBranches	Does models should assume branch in the tree linked or unlinked across partition. 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.
AlphaForGeoks	Risk thershold to consider convergence reached. Should be a float between 0 and 1. It is not advised to take number too small being the null hypothesis the one that interest the researcher ( overlap between the different run of mrbayes).

Processors (3)

Name	Type	Description
DefineAndSubmit_Phylogenetic_infer	workflow
RetrieveANDValidatePhylogenetic_infer	workflow
Concatenate_two_strings	localworker	Script output = string1 + string2;

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 (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 found in www.itol.de
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
Log	Log file of all application used in the workflow. For each external website is reported the name of the application , the jobid required to track error on the service provvider and the last 200line of the standardouput+standardError of the application as view by the local system where the job was run.
PartitionFinderDetails	Path were to retrieve all the detials of the partitionfinder software
GeoKSDetails	Path were to get all details of convergence test calculation.

Datalinks (24)

Source	Sink
PossiblePartition	DefineAndSubmit_Phylogenetic_infer:PossiblePartition
MSA_fasta	DefineAndSubmit_Phylogenetic_infer:MSA_fasta
StatCriterium	DefineAndSubmit_Phylogenetic_infer:StatCriterium
MCMCMCGenerations	DefineAndSubmit_Phylogenetic_infer:MCMCMCGenerationNumber
NumberRuns	DefineAndSubmit_Phylogenetic_infer:NumberRuns
Filename	DefineAndSubmit_Phylogenetic_infer:FileName
LinkingBranches	DefineAndSubmit_Phylogenetic_infer:LinkingBranches
DefineAndSubmit_Phylogenetic_infer:JobID	RetrieveANDValidatePhylogenetic_infer:JobID
DefineAndSubmit_Phylogenetic_infer:NexusFileName	RetrieveANDValidatePhylogenetic_infer:NexusFileName
AlphaForGeoks	RetrieveANDValidatePhylogenetic_infer:AlphaForGeoKS
SampleSize	RetrieveANDValidatePhylogenetic_infer:SampleSize
RetrieveANDValidatePhylogenetic_infer:Log	Concatenate_two_strings:string2
DefineAndSubmit_Phylogenetic_infer:Log	Concatenate_two_strings:string1
RetrieveANDValidatePhylogenetic_infer:Plot	Plot
RetrieveANDValidatePhylogenetic_infer:newickTree	newickTree
RetrieveANDValidatePhylogenetic_infer:GeoKS_Result	Geoks
RetrieveANDValidatePhylogenetic_infer:URL_Output_file	PhyloInferenceOutput
RetrieveANDValidatePhylogenetic_infer:TreeVisualization	ViewTree
RetrieveANDValidatePhylogenetic_infer:MrbayesOutput	MrBayesOutput
RetrieveANDValidatePhylogenetic_infer:xmlTest	DetailsPPtest
DefineAndSubmit_Phylogenetic_infer:PartitionFinderOutput	PartitionFinderOutput
Concatenate_two_strings:output	Log
DefineAndSubmit_Phylogenetic_infer:PartitionFinderDetails	PartitionFinderDetails
RetrieveANDValidatePhylogenetic_infer:convergence	GeoKSDetails