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    lsadt

    DISCLAIMER

    This file has been automatically converted from the original documentation for easy use inside the ARB help system. Differences compared with the original documentation are unintentionally caused by the conversion process. In doubt please refer to the original documentation!

     

    DOCUMENTATION

    DeSoete Tree fit

    This program uses a least squares fitting method to determine additive trees from a given distance matrix. The tree generated is passed back in Newick format. The prefered method of displaying the phylogenetic results is in TreeTool.
    LEAST SQUARES ALGORITHM FOR FITTING ADDITIVE TREES TO PROXIMITY DATA
    GEERT DE SOETE  --  VERSION 1.01 - FEB. 1983
                        VERSION 1.02 - JUNE 1983
                        VERSION 1.03 - JULY 1983
    'C' version by Michael Macuikenas, University of Illinois
    REFERENCE: DE SOETE, G. A LEAST SQUARES ALGORITHM FOR FITTING
       ADDITIVE TREES TO PROXIMITY DATA. PSYCHOMETRIKA, 1983, 48,
       621-626.
       DE SOETE, G. ADDITIVE TREE REPRESENTATIONS OF INCOMPLETE
       DISSIMILARITY DATA. QUALITY AND QUANTITY, 1984, 18,
       387-393.
    REMARKS -------
    1. THE PROGRAM USES SUBROUTINES FROM THE PORT LIBRARY FOR ERROR HANDLING, DYNAMIC STORAGE ALLOCATION AND SPECIFICATION OF MACHINE-DEPENDENT CONSTANTS. CF. FOX, P.A., HALL, A.D., & SCHRYER, N.L.
      • THE PORT MATHEMATICAL SUBROUTINE LIBRAY. ACM TRANS. ON MATH. SOFTW., 1978, 4, 104-126.
      • ALGORITHM 528. FRAMEWORK FOR A PORTABLE LIBRARY. ACM TRANS. ON MATH. SOFTW., 1978, 4, 177-188.

    2. UNIFORMLY DISTRIBUTED RANDOM NUMBERS ARE GENERATED BY A PROCEDURE DUE TO SCHRAGE. CF. SCHRAGE, L. A MORE PORTABLE FORTRAN RANDOM NUMBER GENERATOR. ACM TRANS. ON MATH. SOFTW., 1979, 5, 132-138.
    3. SUBROUTINES VA14AD AND VA14AC ARE ADAPTED FROM THE HARWELL SUBROUTINE LIBRARY (1979 EDITION).
    4. ALTHOUGH THIS PROGRAM HAS BEEN CAREFULLY TESTED, THE AUTHOR DISCLAIMS ANY RESPONSABILITY FOR POSSIBLE ERRORS.