Parser-3.0.20
Parser-3.0.20 is an Agave app for running parse, which is required to run ExaML (Exascale Maximum Likelihood code for phylogenetic inference on supercomputers using MPI). Parse converts an alignment file in relaxed phylip format (as used for RAxML) into a binary file format that can be read by ExaML. The main reason for this is to allow ExaML to read this file faster and not waste any valuable parallel computing time for this simple pre-processing task.
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parser-3.0.20 requires an input alignment in relaxed PHYLIP format. In addition, if your analysis includes partitions, you must upload a partition file. For the syntax of this file please consult the RAxML manual.
Test Data
Use
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the
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nucleotide
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alignment
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49
and
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the
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partion
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file
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49.model
as
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test
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data.
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They
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can
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be
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accessed
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by
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navigating
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to:
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'Community Data'>iplantcollaborative>example_data/ExaML/parse |
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- Run the test analysis using default parameters for:
- substitutionModel = GTRGAMMA
- numberOfRuns=100
- outputFileName=nwk
- parsimonyRandomSeed=123445 (can change this - it will not affect results)
- additionalOptions={leave blank}
You SHOULD NOT include flags for options 1-4, as the program automatically adds them.
You can include any other valid RAxML options as a string using the "additionalOptions" parameter. These options will be appended to the end of the required options 1-4. When specifying additional options, you MUST include the flag, as specified in the RAxML manual. If your options require an input file, be sure to include it in the Inputs section.
Do not use the number of threads (-T) option with this app.
- substitution model/type of data: DNA
- Output file base name: 49
Output File(s)
- Expect the following output files:
- dna.agave.phylog: copy log of activity by the input file
- agave-$longrandomstring.err: standard error
- agave-$longrandomstring.out: standard outputAgave API that ran the app
- 49: the input alignment
- 49.binary: the output of the program. Use this file as input to ExaML
- 49.model: the input partition model
- RAxML_info.nwk49: Information about the model and algorithm used and how RAxML the program was called. The final GAMMA-based likelihood(s) as well as the alpha shape
parameter(s) are printed to this file.
- RAxML_log.nwk.RUN.0 - RAxML_log.nwk.RUN.99: A file that prints out the time, likelihood value of the current tree after each
iteration of the search algorithm. In the last line it also contains the final likelihood value of the final tree topology of each run.
- RAxML_parsimonyTree.nwk.RUN.0 - RAxML_parsimonyTree.nwk.RUN.99: Contains the randomized parsimony starting tree if the program has not been provided a starting tree.
- RAxML_result.nwk.RUN.0 - RAxML_result.nwk.RUN.99: Contains the final tree topology of the current run.
- RAxML_bestTree.nwk: Contains the best-scoring ML tree of a thorough ML analysis.This file also contains an estimate of the memory required to run your ExaML analysis.
- $longrandomstring.err: standard error
- $longrandomstring.out: standard output