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Created: 2013-02-20 14:16:25
Last updated: 2014-06-13 13:54:56
Phylogenetic inference with MrBayes. The the model of evolution is defined with the help of Graphich User Interface (GUI) on the web page, while inference is validated with a 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)
| Define with GUI, infer and validate Phylogeny - short run |
Descriptions (1)
| Phylogenetic inference with MrBayes. The the model of evolution is defined with the help of Graphich User Interface (GUI) on the web page, while inference is validated with a test of MCMC convergence (GEOKS) and fit of the model on the data (Posterior Predictive test) |
Dependencies (0)
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 (7)
| 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 |
|
| PhyloInferenceComplete |
|
| MrBayesOuput |
|
| DetailsPPtest |
|
Datalinks (9)
| Source |
Sink |
| DefineAndSubmit_Phylogenetic_infer:JobID |
RetrieveANDValidatePhylogenetic_infer:JobID |
| DefineAndSubmit_Phylogenetic_infer:NexusFileName |
RetrieveANDValidatePhylogenetic_infer:NexusFileName |
| RetrieveANDValidatePhylogenetic_infer:Plot |
Plot |
| RetrieveANDValidatePhylogenetic_infer:newickTree |
newickTree |
| RetrieveANDValidatePhylogenetic_infer:GeoKS_Result |
Geoks |
| RetrieveANDValidatePhylogenetic_infer:TreeVisualization |
TreeVisualization |
| RetrieveANDValidatePhylogenetic_infer:URL_Output_file |
PhyloInferenceComplete |
| RetrieveANDValidatePhylogenetic_infer:MrbayesOutput |
MrBayesOuput |
| RetrieveANDValidatePhylogenetic_infer:xmlTest |
DetailsPPtest |
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License
All versions of this Workflow are
licensed under:
Version 5
(of 12)
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