Classes for the support of yn00.
Yang and Nielsen 2000, estimating synonymous and nonsynonymous substitution rates in pairwise comparison of protein-coding DNA sequences.
- exception Bio.Phylo.PAML.yn00.Yn00Error¶
yn00 failed. Run with verbose=True to view yn00’s error message.
- class Bio.Phylo.PAML.yn00.Yn00(alignment=None, working_dir=None, out_file=None)¶
An interface to yn00, part of the PAML package.
- __init__(self, alignment=None, working_dir=None, out_file=None)¶
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.
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.
- read_ctl_file(self, ctl_file)¶
Parse a control file and load the options into the yn00 instance.
- run(self, ctl_file=None, verbose=False, command='yn00', parse=True)¶
Run yn00 using the current configuration.
If parse is True then read and return the result, otherwise return None.
Parse a yn00 results file.