Decay Indices Update

[Clabaugh, Jerod Biology]

12 April 1996

Hello all:

A year ago, I posted responses to a query concerning 'Decay indices' or
'Bremer support'.  I have gotten many requests for my original posting and
would like to post a revised version now, including information on where to
obtain the latest version of a computer program for computing these indices.


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To all interested parties concerning
'Decay Indices' or 'Bremer support'.

PRINT THIS NOW! OR CLICK SAVE AS..(TEXT) FOR LATER REFERENCE

Citations follow in sequential order (I think):

Bremer, K. 1988. The limits of amino acid sequence data in Angiosperm
phylogenetic reconstruction. Evolution. 42: 795-803.

"The "Decay Index" name was first used  in:

Donoghue, M. J., R. G. Olmstead, J. F. Smith, and J. D. Palmer. 1992.
Phylogenetic relationships of Dipsacales based on rbcL Sequences. Ann.
Missouri Bot. Gard. 79: 333-345 (Eriksson, pers. comm.)"

THEN:

 Kallersjo, M,  J. S. Farris, A. G. Kluge, and C. Bult. 1992 Skewness and
permutation. Cladistics 8: 275-287 .
-attempted to change the name of the index to "Bremer support" in a footnote
of their paper.

ADDITIONAL PAPERS INCLUDE:

-  a definition of the decay indices in Mishler et. al., 1992 Bryologist
   95: 172-180. (Savolainen, pers. comm.)

Bremer K. & Humphries, C.J. (1993). Generic monograph
of the Asteraceae-Anthemideae. Bull. nat. Hist. Mus. Lond. 23: 71-177
(Parnell, pers. comm.)

Bremer, K. 1990.  Combinable component consensus.Cladistics 6:369-372.

INFORMATION ON THE QUALITATIVE USAGE OF DECAY INDICES(i.e., Total support
Index(ti)) CAN BE FOUND IN:

Bremer, K. 1994. Branch Support and Tree Stability. Cladistics 10:295-304.


Explanation of AutoDecay's creation taken from a message from Torsten
Eriksson, the Author of the program:

" One of the more interesting additions to the method appear with the
version 3 of PAUP: [Swofford, D. L. 1993. PAUP: Phylogenetic Analysis Using
Parsimony (Computer program). Smithsonian Institution, Washington.]
In which, Swofford incorporated constraints which could be used as reverse
constraints. This made it possible to find the answer to the question: How
long is the shortest tree lacking this particular node?
It was the amount of work invested in doing this for each node in a tree
that made me create AutoDecay. Of course, it would be better to
have this included in PAUP but as long as this is not the case, you're
welcome to use AutoDecay. As far as I know there is no other program but
PAUP that can use constraints or reverse constraints.
Torsten.Eriksson at botan.su.se"


Both programs can be gotten from Dr. Eriksson at the above email address or
from his web page (http://www.botan.su.se/Systematik/Folk/Torsten.html)

BECAUSE OF THE TREMENDOUS INTEREST I HAVE RECIEVED
AND BECAUSE DR. ERIKSSON"S WEBSITE IS SLOW, I AM
NOW PROVIDING A MIRROR SITE FOR THESE PROGRAMS
AS WELL AS OTHER PHYLOGENETIC PROGRAMS(treeview) USED IN
CONJUNCTION WITH AUTODECAY.

Using Netscape, direct it to ftp://128.97.40.127/pub/autodecay


AutoDecay 3.03 is a C program compiled for the 68k Mac (will work on PPCMac)

AutoDecay 2.9.3 is a hypercard stack for the 68kMac + PPCMac.
Needs AT LEAST Hypercard player 2.0.

Dr. Eriksson says...

"*  The HyperCard version has changed (2.9.2) and now has some more features
than the C-version. The most important change is that it is now possible to
view and print trees with decay indices on it. This is done with the help of
Rod Page's Treeview prgm (http://taxonomy.zoology.gla.ac.uk/rod/treeview.html)

The second difference from the C-version is the possibility of running
PAUP analyses in parallel which can save time if you have large trees with
many nodes and/or messy data sets."


***Dr. Eriksson only requests that the program NOT be sold and I feel he
should be acknowledged if this program is used in the generation of Decay
Indices for use in publication.***

***I have also been made aware that Dr. Doug Eernisse(DEernisse at Fullerton.edu)
has a program in his DNA stacks program which does something similar.  You
should contact him for more information or see his webpage
   (http://biology.fullerton.edu/people/faculty/doug-eernisse/)****

Let me know if anyone needs more info or help dowloading/running Dr.
Eriksson's executables.

Cheers,


Jerod Clabaugh
Dept. of Biology
University of California
621 Circle Drive South
Los Angeles, CA 90095-1606
voice: (310) 206-7885
FAX: (310) 206-3987
E-Mail: JerodcC at biology.lifesci.ucla.edu
www: http://128.97.40.127/jerod/jerod.html