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__(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()

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(ctl_file): Parse a control file and load the options into the yn00 instance.

run(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.