Module: rje_paml Description: RJE PAML Wrapper Module Version: 0.0 Last Edit: 10/06/09

Copyright © 2009 Richard J. Edwards - See source code for GNU License Notice

Imported modules: rje rje_seq rje_zen

See SLiMSuite Blog for further documentation. See rje for general commands.

Function

This module is a simple wrapper and parser for PAML. If PAML results files exist, a given input file will be skipped (unless force=T) and results read in. The tabulated results file will be overwritten, however.

Commandline

Input/Output Options

batch=LIST : List of files to batch run on ['*.fas']
resdir=PATH : Directory for results output ['PAML/']
basefile=X : Base for names of results files ['pamlres']
stripgap=X : Strip codons with gaps in at least X sequences [2]

PAML Analyses Options

dnds=T/F : Whether to extract DN/DS results from outfile [True]

PAML & System Options

pamlpath=PATH : Path to PAML package exectuables [./]
ctlfile=FILE : PAML control file to use ['codeml.ctl']
infile=FILE : Name for PAML sequence input file ['infile']
outfile=FILE : Name of PAML output file ['mlc']

See also rje.py generic commandline options.

History Module Version History

    # 0.0 - Initial Compilation.