Bio.Phylo.PAML.yn00 module¶
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
¶ Bases:
OSError
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)¶ Bases:
Bio.Phylo.PAML._paml.Paml
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.
-
write_ctl_file
(self)¶ 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.
-
-
Bio.Phylo.PAML.yn00.
read
(results_file)¶ Parse a yn00 results file.