Pack: Perform Long Bayesian Phylogenetic Inference

Created: 2013-02-20 14:59:31      Last updated: 2015-06-12 13:48:46
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Title: Perform Long Bayesian Phylogenetic Inference


Information Description

Phylogenetic inference with mrbayes requires long calculation. So is not possible to keep the taverna engine on for the time required for the analysis. The solution is to break the Workflow in 2 part: before and after submission to mrbayes service.

In this pack there are 3 workflows for submission:

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

The pack includes one retrieval workflow that perform 2 validations of the inference,  one on the numerical integration (GeoKS) and one on the fit of the model (Posterior Predictive Test)

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

 

Subscribe to RSS feed for items in this pack feed Download Information Items (4)

  • Internal item

    Workflow: Bayesian Phylogenetic Inference: Select Model - Submission (Saverio Vicario)

    Added by Saverio Vicario ... more than 1 year ago (2013-02-20 15:00:36)

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  • Internal item

    Workflow: Bayesian Phylogenetic Inference: Select Model For Me - Submission (Saverio Vicario)

    Added by Saverio Vicario ... more than 1 year ago (2013-02-20 15:00:22)

    moreExpand

  • Internal item

    Workflow: Bayesian Phylogenetic Infererence: Evaluate MrBayes Run (Saverio Vicario)

    Added by Saverio Vicario ... more than 1 year ago (2013-02-20 15:00:48)

    moreExpand

  • Internal item

    Workflow: Bayesian Phylogenetic Infererence: Input Ready - Submission (Saverio Vicario)

    Added by Saverio Vicario ... more than 1 year ago (2013-02-20 15:00:04)

    moreExpand



Information Relationships (3)

  1. Bayesian Phylogenetic Inference: Select Model - Submission is an input to Bayesian Phylogenetic Infererence: Evaluate MrBayes Run .
  2. Bayesian Phylogenetic Inference: Select Model For Me - Submission is an input to Bayesian Phylogenetic Infererence: Evaluate MrBayes Run .
  3. Bayesian Phylogenetic Infererence: Input Ready - Submission is an input to Bayesian Phylogenetic Infererence: Evaluate MrBayes Run .


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