SelectingEvolutionaryModelWithPartFinder
Created: 2013-12-11 13:44:06
Last updated: 2014-12-01 11:00:00
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Authors (1)
| saverio vicario
giacinto donvito |
Titles (1)
| Selecting Evolutionary Model for a phylogenetic inference using partitionFinder program |
Descriptions (1)
| Selecting Evolutionary Model for a phylogenetic inference using partitionFinder program. The program (http://www.robertlanfear.com/partitionfinder/) search best candidate model that satisfy need of the different partition. The program do not explore all possible model that could be implemented in mrbayes, in fact it do not allow for link of subsitution matrix but different base frequency across partitions, or to link branch lenght across some partitions but not all. For a greater fine tuning of model the user is advised to use the GUI interface present in the phylogenetic inference pipeline |
Dependencies (0)
Inputs (7)
| Name |
Description |
| MSA_fasta |
Multiple Sequence Alignment (MSA) in fasta format
|
| PossiblePartition |
Partitioning of the MSA using nexus/raxml -like syntax
|
| StatCriterium |
|
| LinkingBranches |
|
| NumberRuns |
Number of independent Runs ( at least 2) [an integer]
|
| MCMCMCGenerationNumber |
|
| Token |
|
Processors (12)
| Name |
Type |
Description |
| Call_PartitionFinder |
component |
|
| ServiceName |
stringconstant |
ValuePartitionFinder |
| Concatenate_two_strings |
localworker |
Scriptoutput = string1+" "+ string2; |
| File_name_value |
stringconstant |
Valuepartition_finder.cfg |
| File_name_value_1 |
stringconstant |
Valuetest.phy |
| ModelsetGUI |
workflow |
|
| MrBayesParser |
externaltool |
|
| fasta2phy |
externaltool |
|
| Logger |
localworker |
Scriptoutput = "Application:"+Name +"\n"+"JobID:" +JobID+"\n"+"StdError:"+StdError; |
| JSTWebDav3Input |
component |
|
| JSTWebDav3Input_2 |
component |
|
| Flatten_List |
localworker |
Scriptflatten(inputs, outputs, depth) {
for (i = inputs.iterator(); i.hasNext();) {
element = i.next();
if (element instanceof Collection && depth > 0) {
flatten(element, outputs, depth - 1);
} else {
outputs.add(element);
}
}
}
outputlist = new ArrayList();
flatten(inputlist, outputlist, 1); |
Outputs (4)
| Name |
Description |
| Path |
Path to obtain full folder of ouput of PartitionFinder
|
| PartitionFinderOuput |
Text output of best model description of PartitionFinder program
|
| MrBayesInput |
Input file for MrBayes in nexus format both data and model using mbayes dialect
|
| Log |
|
Datalinks (28)
| Source |
Sink |
| ServiceName:value |
Call_PartitionFinder:Name |
| Concatenate_two_strings:output |
Call_PartitionFinder:Argument |
| JSTWebDav3Input:REST_Service_redirection |
Concatenate_two_strings:string2 |
| JSTWebDav3Input_2:REST_Service_redirection |
Concatenate_two_strings:string1 |
| PossiblePartition |
ModelsetGUI:GenePartition |
| StatCriterium |
ModelsetGUI:StatCriterium |
| LinkingBranches |
ModelsetGUI:LinkingBranch |
| ModelsetGUI:BL |
MrBayesParser:BL |
| ModelsetGUI:PartitionDef |
MrBayesParser:PartDef |
| Call_PartitionFinder:Standardoutput |
MrBayesParser:PartFinder |
| fasta2phy:MSAphy |
MrBayesParser:MSAphy |
| MCMCMCGenerationNumber |
MrBayesParser:nGen |
| NumberRuns |
MrBayesParser:nRun |
| MSA_fasta |
fasta2phy:MSAfasta |
| Call_PartitionFinder:JobID |
Logger:JobID |
| ServiceName:value |
Logger:Name |
| Call_PartitionFinder:StandardError |
Logger:StdError |
| File_name_value:value |
JSTWebDav3Input:File_name |
| ModelsetGUI:Test |
JSTWebDav3Input:InputBody |
| Token |
JSTWebDav3Input:Token |
| File_name_value_1:value |
JSTWebDav3Input_2:File_name |
| Token |
JSTWebDav3Input_2:Token |
| fasta2phy:MSAphy |
JSTWebDav3Input_2:InputBody |
| Logger:output |
Flatten_List:inputlist |
| Call_PartitionFinder:Output_Path |
Path |
| Call_PartitionFinder:Standardoutput |
PartitionFinderOuput |
| MrBayesParser:MrBayesBlock |
MrBayesInput |
| Flatten_List:outputlist |
Log |
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Version 9
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