Random Cladistics 3.0 [and still freely ftp-able]

Mark Siddall mes at zoo.toronto.edu
Fri Jul 14 20:24:24 EST 1995

This message announces the release of Random Cladistics 3.0, software
designed for performing a variety of randomization-based data 
manipulations in the field of phylogenetic inference.

It is available free via anonymous ftp to zoo.toronto.edu (or 
zoo.utoronto.ca) in the directory "pub" as the self-extracting DOS
utility "random.exe", please transfer in binary mode.

1) "slipshod" - as per bootstrap but by marking scopes (i.e., strings
    of contiguous characters) for inclusion/exclusion - output includes
    data on frequency of clade support (as per bootstraps), as well as
    a table of effects of inc/exclusion of regions on length/RI/#trees.
2) JOYRIDE - random-addition sequence replicates for avoiding islands
    or penninsulae of trees - output includes all most-optimal trees
    found as well as table of performance in each attempt.
3) TRECMP - relatively versatile option for comparing one tree with many
   saved in a treefile, for looking for how frequently two or more
clades appear SIMULTANEOUSLY in bootstrap replicates (in fact you can
look for the whole of a tree), for assessing levels of tree-balance,
etc etc etc
4) MUCH improved on-line help on RC and on Hennig86 including menubars
    and word-searches etc.
5) TORA - for converting Hennig86 or #nexus format files for input to
   Farris' Rapid-Nucleotide-Analysis (RA) program.
6) Taxon Jacknifing including JMI clade support values now accepts 
   matrices of any size like the rest of the algorithims.

THINGS RC 2.1 did and 3.0 still does:
1) regular old bootstrapping
2) other kinds of character-manipulation like deltion
3) PTP
4) random-tree-histograms
5) PCP - confidence in coevolution.

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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