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rje_price V0.0

Experimental Price Equation Tool

Module: rje_price
Description: Experimental Price Equation Tool
Version: 0.0
Last Edit: 05/01/09

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


Imported modules: rje rje_seq rje_sequence rje_zen


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

Function

Current fitness scores:

Commandline

INPUT OPTIONS

seqin=FILE : Input sequence alignment in fasta format (over-rides batch=LIST) [None]
batch=LIST : List of alignment files to use as input [*.fas,*.fasta]
query=X : Identifier of query sequence [None]
dna=T/F : Whether sequences are DNA or protein [True]

PRICE EQUATION OPTIONS

fitness=X : Fitness measurement [cons]
phenotype=X : Phenotype measurement [cons]
seqgroup=X : Sequence grouping method [triplets]
qrygaps=T/F : Whether to include gaps in the query sequence as positions to score [False]
special=X : Instigate special run, e.g. allbyall [None]
normfit=X : Normalise fitness to have mean of 1 [False]
weighted=T/F: Weight the mean covariance by size of group [True]

OUTPUT OPTIONS

resfile=FILE: Results file [price.tdt]
append=T/F : Append results file if already present [True]


See also rje.py generic commandline options.

History Module Version History

    # 0.0 - Initial Compilation.

© 2015 RJ Edwards. Contact: richard.edwards@unsw.edu.au.