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Created: 2013-02-20 13:41:39
Last updated: 2014-04-13 19:25:37
Phylogenetic inference with MrBayes. Perform inference and test of MCMC convergence (GEOKS) and fit of the model on the data (Posterior Predictive test)
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Authors (1)
| saverio vicario
giacinto donvito
bachir balech
|
Titles (1)
| Infer and validate Phylogeny - short run |
Descriptions (1)
| Phylogenetic inference with MrBayes. Perform inference and test of MCMC convergence (GEOKS) and fit of the model on the data (Posterior Predictive test) |
Dependencies (0)
Inputs (4)
| Name |
Description |
| NexusFile |
MSA (Multiple Sequence Alignment) and model of evolution in nexus format with Mrbayes block
|
| FileName |
A string. The File Name of the nexus file used as input
|
| AlphaForConvergenceTest |
A float number between 0 and 1. It represent the minimal probability of the null hypothesis ( Convergence) that the user want to accept. Remind that this is not a classical test because user are interested to the null hypothesis (Convergence) and not in the Alternative one.
|
| SampleSizeForPPtest |
an integer that indicate the number of Item of the sample from the Posterior distribution of the Bayesian phylogenetic inference that are used to build the null distribution of the Posterior Predictive Test.
Take care that this number is smaller than ngen/samplefreq, where this two values are the parameters of the mcmc option within mrbayes block of the nexus file. If samplefreq is not specified the default value in mrbayes 3.1.2 is 100.
|
Processors (2)
| Name |
Type |
Description |
| DefineAndSubmit_Phylogenetic_infer |
workflow |
|
| RetrieveANDValidatePhylogenetic_infer |
workflow |
|
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 (9)
| 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 |
Restul of the GeoKS test of convergence. XML format
|
| TreeVisualization |
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
|
| PhyloInferenceOuput |
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
|
| DetailsPPtest |
Restul of the GeoKS test of convergence. XML format
|
| GeoKSDetails |
Path were to get all details of convergence test calculation.
|
| 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.
|
Datalinks (15)
| Source |
Sink |
| NexusFile |
DefineAndSubmit_Phylogenetic_infer:NexusFile |
| FileName |
DefineAndSubmit_Phylogenetic_infer:FileName |
| DefineAndSubmit_Phylogenetic_infer:JobID |
RetrieveANDValidatePhylogenetic_infer:JobID |
| DefineAndSubmit_Phylogenetic_infer:NexusFileName |
RetrieveANDValidatePhylogenetic_infer:NexusFileName |
| SampleSizeForPPtest |
RetrieveANDValidatePhylogenetic_infer:SampleSize |
| AlphaForConvergenceTest |
RetrieveANDValidatePhylogenetic_infer:AlphaForGeoKS |
| RetrieveANDValidatePhylogenetic_infer:Plot |
Plot |
| RetrieveANDValidatePhylogenetic_infer:newickTree |
newickTree |
| RetrieveANDValidatePhylogenetic_infer:GeoKS_Result |
Geoks |
| RetrieveANDValidatePhylogenetic_infer:TreeVisualization |
TreeVisualization |
| RetrieveANDValidatePhylogenetic_infer:MrbayesOutput |
MrBayesOutput |
| RetrieveANDValidatePhylogenetic_infer:URL_Output_file |
PhyloInferenceOuput |
| RetrieveANDValidatePhylogenetic_infer:xmlTest |
DetailsPPtest |
| RetrieveANDValidatePhylogenetic_infer:convergence |
GeoKSDetails |
| RetrieveANDValidatePhylogenetic_infer:Log |
Log |
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License
All versions of this Workflow are
licensed under:
Version 6
(of 8)
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