RANDOM CLADISTICS SOFTWARE for DOS (If you want it)!

Mark Siddall mes at zoo.toronto.edu
Fri Mar 25 00:36:33 EST 1994


A problem facing many cladists is the fact that PAUP 3.0 is not available
     for pc's as yet, being only available for Macs.

This prevents pc users from being able to take advantage of the ancillary
     routines PAUP provides such as random tree length histograms and the
     associated g-stats, and Felsenstein's Bootstrap (unless you have
     PHYLIP).

By way of circumventing this, I have created a menu driven software
     package that performs a variety of options on data sets by running
     Hennig86 as a daughter process.

The software is written in C++ for the DOS environment and runs quite
     fast.

I am willing to make this package available via our anonymous ftp site
     here in Toronto but require some feedback in order to justify long-
     term storage to our sysops etc.  (I'm leaving the dept. next month)

If you are interested please fire me quick note to that effect at
     mes at zoo.toronto.edu

FOR THE SOFTWARE TO BE USEFUL YOU MUST HAVE A COPY OF HENNIG86.  I CANNOT
     MAKE THAT AVAILABLE AS IT IS COPYRIGHTED BY J. S. Farris.

Here's what the package will do:

1. Permutation Tail Probability Test 
     - Faith and Cranston
     - not yet available in PAUP

2. Bootstrapping
     - Felsentein
     - incl. automated check of all monophyletic groups in "true" tree(s)
     - 1000 bootstrap pseudoreplicates and analysis possible in less than
       a couple of hours (depending on complexity of data and processor).

3. Jacknifing
     - Lanyon (well... sort of)
     - incl. analysis of effect of deleting taxa on length/RI/#MEPT

4. Random Tree Histograms
     - generates trees according to Markovian tree-building process
     - outputs freq. distrib., mean, variance, SD, G1 (skewness), G2
       (kurtosis), and probability values for skew and kurtosis.
     - to the best of my knowledge, PAUP does not do G2 or tests of 
       significance of skew or significance of kurtosis.

5. User-friendly Hennig86 guide.

6. Help on above software.

and a couple of other things I'm still playing with.


With any luck, I can have it all set up within a couple of weeks.
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