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rje_dismatrix V2.10

Distance Matrix Module

Module: rje_dismatrix
Description: Distance Matrix Module
Version: 2.10
Last Edit: 09/02/14

Copyright © 2007 Richard J. Edwards - See source code for GNU License Notice


Imported modules: rje rje_zen


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

Function

DisMatrix Class. Stores distance matrix data and contains methods for extra calculations, such as MST. This module is primarily for use within other modules but can be used for slmple distance matrix conversions and UPGMA tree construction.

Commandline

loadmatrix=FILE : Loads a matrix from FILE [None]
symmetric=T/F : Whether the matrix should be symmetrical (e.g. DisAB = DisBA) [False]
outmatrix=X : Type for output matrix - text / mysql / phylip / png
nsf2nwk=T/F : Whether to convert extension for Newick Standard Format from nsf to nwk (for MEGA) [False]

History Module Version History

    # 0.0 - Initial Compilation.
    # 1.0 - Working version used in several programs.
    # 2.0 - Updated module inline with newer modules and layout. Incorporation of Minimum Spanning Tree.
    # 2.1 - Attempted in incorporate pylab heatmap generation from distance matrix.
    # 2.2 - Added loading of matrix from GABLAM-style database file.
    # 2.3 - Added UPGMA method.
    # 2.4 - Added UPGMA branch length return.
    # 2.5 - Added PNG output based on rje_slimhtml.
    # 2.6 - Added nsf2nwk=T/F - Whether to convert extension for Newick Standard Format from nsf to nwk (for MEGA)
    # 2.7 - Added reading of BLOSUM matrix and standalone functionality. Removed pylab heatmap from docstring.
    # 2.8 - Slightly modified clustering output.
    # 2.9 - Modified PNG output to use rje_tree code instead. Added Graph output using rje_ppi.
    # 2.10- Minor modifications for SLiMCore UPC.

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