REVISED SOFTWARE: Random Cladistics 2.1.1

Mark Siddall mes at zoo.toronto.edu
Tue Mar 7 17:16:51 EST 1995


Random Cladistics 2.1.1 is software that is available free of charge to 
anyone who wants it.
With it you can bootstrap/jackknife/PTP/generate random tree histograms
and calculate confidence values on cladistic coevolutionary questions.
All of this for DOS users!! 
Random Cladistics 2.1.1 is ready for anonymous ftp from zoo.toronto.edu.
The operative directory is pub.
The filename is random.exe as before.
Please transfer in binary mode.
PLEASE DISCARD ALL FILES FROM PREVIOUS VERSIONS!! They are not compatible.

random.exe is a self extracting utility and will explode the version 2.1.1
executables as well as a morphological data file, a sequence data file,
other related data files, a on-line and MS-WRD for DOS quide to 
Random Cladistics as well as Hennig86 (help on it, not the executable).

IMPROVEMENTS OVER VERS 2.0

PTP.EXE
*       for one, it actually works now! Previously caught in a for(;;).
*       no longer need to know how long your true trees are a priori.  Your
        unpermuted data set is the first to be executed.
*       previous limits on character matrix size eliminated: memory 
        dynamically
        allocated to exact size requirenment
*       titles automatically parsed and included; no more prompting for "is
        there a title?"
*       better use of memory: only hold one matrix in memory
*       faster randomization routine by cycling through states in a column
        rather than swapping from matrix to matrix and having to hit and miss
        previous states
*       minimalist output to screen when surfing through results - 
        improved run
        time
*       previously had to pass through results and rewind as many times 
        as (maxsteps - #char).  Now only two passes: one to find max-steps and
        min-steps, the other to send all freq. into dynamically allocated
        memory (your hard drive will thank you).
*       Kallersjo et al. distributional estimate (a*) of true tail 
        distribution reported
*       independence of calculating algorithms MEPTs and PTP trees


 HEYJOE.EXE
*       name improved: previously (and unimaginitively) boot.exe, presenting
        name conflict with early versions of Phylip.  Out of deference to
        Felsenstein, as well as to Jimmy (not Carpenter) my having 
        bastardized into "Hey O.J." an otherwise groovin' tune, the name 
        was changed. (words to Hey O.J. available on request)
*       titles automatically parsed
*       previous limits on character matrix size eliminated: memory 
        dynamically allocated to exact size requirenment
*       independence of tree calculating algorithms can now be thorough 
        on your real trees and heuristic on your bootstrap trees
*       new options including: minimum bootstrap values; code-word 
        "arbre" for reading in previously saved treefiles tsaved earlier 
        from Hennig86, used as a starting point for bb or for tree 
        compression only; code-word "rcd" for a random character deletion 
        approach either with or without arbre;
*       minimalist screen output saves on run time
                CHKBOOT.EXE (autoinvoked by heyjoe)
        *       laborious time-intensive file modification period is gone!
        *       minimalist screen output
        *       non-redundant clade checking!!!
        *       now replaces reboot.exe from vers. 2.0 as well and is 
                smart to the difference of whether you are re-checking saved 
                replicates
        *       massively improved run-time.

TREES.EXE
*       titles parsed automatically
*       prompted for coding options now (what a bone-head omission last 
        time).
*       x-based histograms eliminated; data only
*       inclusion of cautionary tale regarding p-values on g-stats


LANYON.EXE              DANRAN.EXE                      RND.EXE
        titles parsed           unmodified              modified to accept
                                                        HEYJOE.EXE
        CHKLAN.EXE
           minimalist screen output

-- 
Mark E. Siddall                "I don't mind a parasite...
mes at vims.edu                    I object to a cut-rate one" 
Virginia Inst. Marine Sci.                     - Rick
Gloucester Point, VA, 23062




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