MacClade

Dan Jacobson danj at merlot.gwu.edu
Thu Oct 29 11:32:34 EST 1992


jthomaso at nmsu.edu (THOMASON) writes:

>  Does anyone know where I can get a hold of a copy of MacClade
>(cladistics)? analyzation software for the common mac?  I've been
>checking the retailers and noone seems to be able to get a grip on it
>around here atleast. Please reply via EMAIL....  Thank You


You can obtain MacClade by anonymous ftp from the following sites:

Host fly.bio.indiana.edu

    Location: /molbio/mac
           FILE -rw-r--r--     144646  May 14 1991  macclade.hqx

Host sunbcd.weizmann.ac.il

    Location: /pub/software/mac
           FILE -r--r--r--     144646  May 14 1991  macclade.hqx

Host sunsite.unc.edu

    Location: /pub/academic/bio/molbio/mac
           FILE -r--r--r--     144646  May 14 1991  macclade.hqx


For those of you who aren't familiar with MacClade here's a 
description that Joe Felsenstein (noted phylogeny guru and author of
the PHYLIP package) wrote in his Phylip documentation:



     3.  If you have a Macintosh computer and any  interest  in  discrete-state
parsimony  methods (including DNA and protein parsimony), you should definitely
get MacClade.  As of  this  writing  it  was  distributed  by  Wayne  Maddison,
Department  of Ecology and Evolutionary Biology, University of Arizona, Tucson,
Arizona  85721, U.S.A.  David Maddison and he have produced a program  enabling
you  to  use the mouse-window interface to specify and rearrange phylogenies by
hand, and watch the number of character steps and the distribution of states of
a  given  character  on  the  tree  change as you do so. MacClade is positively
addictive and will give you a much better feel for  the  tree  and  your  data.
It's the closest thing to a phylogeny video game that I have seen.  It has been
influential in spurring the inclusion of interaction and  graphics  into  other
phylogeny  programs.   (I  have tried to supply this functionality in PHYLIP by
incorporating the programs MOVE, DOLMOVE, and DNAMOVE, which act somewhat  like
MacClade).   MacClade  does  not  have a sophisticated search algorithm to find
best trees: it largely relies on you to do it by hand  (which  is  surprisingly
effective),  with  only a local rearrangement algorithm available to improve on
that tree.

     Version 2.1 was released in March 1987.  Version 3,  with  a  spread-sheet
data  editor,  support  for  polytomies, charting facilities, PHYLIP, PAUP, and
HENNIG86 compatibility, and many other  new  features,  is  coming  soon.   The
program  is  originally  written  in  Lightspeed Pascal but is provided in pre-
compiled form, and is available for distribution cost ($6 in North America,  $8
overseas,  or three or four Macintosh diskettes in barter).  It requires a 512K
Macintosh, Macintosh Plus, or larger.  In the near future the  distribution  of
version  3  will  be on a commercial basis by Sinauer Associates of Sunderland,
Massachusetts,  although  versions  1  and  2  will  continue  to   be   freely
distributable.   Version  2  is also available by electronic mail from the EMBL
and Houston net servers which  distribute  free  software  for  molecular  data
analysis, in their Mac software, as a squeezed and then binhexed file.



Best of luck,


Dan Jacobson

danj at chablis.gwu.edu




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