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rje_pam V1.2.1

Contains Objects for PAM matrices

Module: rje_pam
Description: Contains Objects for PAM matrices
Version: 1.2.1
Last Edit: 27/11/15

Copyright © 2005 Richard J. Edwards - See source code for GNU License Notice


Imported modules: rje


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

Function

This module handles functions associated with PAM matrices. A PAM1 matrix is read from the given input file and multiplied by itself to give PAM matrices corresponding to greater evolutionary distance. (PAM1 equates to one amino acid substitition per 100aa of sequence.)

Commandline

pamfile=X : Sets PAM1 input file [jones.pam]
pammax=X : Initial maximum PAM matrix to generate [100]
pamcut=X : Absolute maximum PAM matrix [1000]

Alternative PAM matrix commands

altpam=FILE : Alternative to PAM file input = matrix needing scaling by aafreq [None]
seqin=FILE : Sequence file from which to calculate AA freq for scaling [None]
pamout=FILE : Name for rescaled PAM matrix output [*.pam named after altpam=FILE]

Classes

PamCtrl(rje.RJE_Object):
- Controls a set of PAM matrices.
PAM(pam,rawpamp,alpha):
- Individual PAM matrix.
>> pam:int = PAM distance
>> rawpamp:dictionary of substitution probabilities
>> alpha:list of amino acids (alphabet)


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