Pack: Perform Short Bayesian Phylogenetic Inference

Created: 2013-02-20 15:07:21      Last updated: 2013-08-21 16:09:33
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Title: Perform Short Bayesian Phylogenetic Inference


Information Description

The Pack contain 3 workflows that perform and validate bayesian phylogenetic inference that differ from the kind of input. The pack is called short because the worlflow require that the user need to keep taverna engine always on for the the time of the analysis. This could be quite problematic for large analysis. In this case search help in the "Perform Long Bayesian Phylogenetic Inference" pack

In this pack there are 3 workflows:

1) User locally formatted input file (for details in nexus format for mrbayes http://mrbayes.sourceforge.net/wiki/index.php/Manual_3.2)

2) User is helped by a GUI (graphical user interface) to define an partitioned evolutionary model on user defined MSA (multiple sequence alignment)

3) PartitionFinder define best candidate partitioned evolutionary model based on proposed maximum set of possible partition

Note: a partitioned model is a model that allow different groups of sites (i.e. columns of the MSA) to follow the rule or parameters set of different evolutionary models. MrBayes allows that some of the parameters to be shared across partitions  while other being different. The submit workflow 2 based on the GUI allow to fully take advantage of this features while the submit workflow 3 based on PartitionFinder allow to share across partition optionally  branch length and always the topology

All 3 workflows perform 2 validations on the inference,  one on the numerical integration (GeoKS) and one on the fit of the model (Posterior Predictive Test)

 

Details on the implementation and the scientific relevance could be found in this wiki

Subscribe to RSS feed for items in this pack feed Download Information Items (3)

  • Internal item

    Workflow: Input Ready (Saverio Vicario)

    Added by Saverio Vicario ... more than 1 year ago (2013-02-20 15:07:39)

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  • Internal item

    Workflow: Select Model (Saverio Vicario)

    Added by Saverio Vicario ... more than 1 year ago (2013-02-20 15:07:29)

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  • Internal item

    Workflow: Select Model For Me with components (Saverio Vicario)

    Added by Saverio Vicario ... more than 1 year ago (2013-02-20 15:08:00)

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