|Description:|| Contains Objects for PAM matrices|
|Last Edit:|| 27/11/15|
Copyright © 2005 Richard J. Edwards - See source code for GNU License Notice
See SLiMSuite Blog for further documentation. See
rje for general commands.
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.)
pamfile=X : Sets PAM1 input file [
pammax=X : Initial maximum PAM matrix to generate [
pamcut=X : Absolute maximum PAM matrix [
Alternative PAM matrix commands
altpam=FILE : Alternative to PAM file input = matrix needing scaling by aafreq [
seqin=FILE : Sequence file from which to calculate AA freq for scaling [
pamout=FILE : Name for rescaled PAM matrix output [*.pam named after
- Controls a set of PAM matrices.
- Individual PAM matrix.
>> pam:int = PAM distance
>> rawpamp:dictionary of substitution probabilities
>> alpha:list of amino acids (alphabet)