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object --+ | _paml.Paml --+ | Yn00
This class implements an interface to yn00, part of the PAML package.
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Initialize the Yn00 instance. The user may optionally pass in strings specifying the locations of the input alignment, the working directory and the final output file.
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Dynamically build a yn00 control file from the options. The control file is written to the location specified by the ctl_file property of the yn00 class.
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Parse a control file and load the options into the yn00 instance.
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Run a paml program using the current configuration and then parse the results. Return a process signal so the user can determine if the execution was successful (return code 0 is successful, -N indicates a failure). The arguments may be passed as either absolute or relative paths, despite the fact that paml requires relative paths.
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