PUZZLE 2.3 AVAILABLE

Korbinian Strimmer strimmer at zi.biologie.uni-muenchen.de
Fri Dec 1 09:11:11 EST 1995


                  ====================================
                   PUZZLE VERSION 2.3 NOW AVAILABLE!!
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NEW IN VERSION 2.3:

     * more models for maximum likelihood calculation
       + mtREV model (Adachi-Hasegawa, for proteins encoded on mtDNA)
       + SH model (Schoeniger-von Haeseler, for dependent nucleotides)
     * base frequencies can now be freely specified
     * input format change to PHYLIP INTERLEAVED
     * usability improvements
       + clear error messages
       + remaining time estimations during run
       + all infos about run written down in "puzzle.out" file
       + report of base frequencies
       + nucleotide and protein analysis combined in one program
     * built-in consensus tree routines
     * more supported systems
       + MS-DOS
       + VMS
     * bug fixes (necessary for doing runs with a large number of taxa)
     * algorithmic improvements
       + better quartet handling (what to do if quartet topology is
unclear)
       + better edge selection (random if two edges are equally weighted)
       + no more dependencies from input order
     * one additional Internet server (making downloading more easy)

All these new features are definitely worth the upgrade from version 2.2
(especially the bug fixes :-) !


ABOUT PUZZLE:

PUZZLE is an ANSI C compliant and PHYLIP compatible program that
implements the
quartet puzzling method for reconstructing tree topologies from character
state
data.  Quartet puzzling is a method that applies maximum likelihood tree
recon-
struction to all possible quartets of taxa and subsequently tries to
combine
most of the four-taxa maximum likelihood trees to construct an overall
tree.
Usually there are several possible solutions.  A consensus tree generated
from
the quartet puzzling trees shows nodes that are well supported.  More
details
about the algorithm and on the phylogenetic accuracy will be published
elsewhere
(K. Strimmer and A. von Haeseler, 1996). 

PUZZLE supports all popular models of sequence evolution of nucleotides
and
proteins.  PUZZLE is platform independent and runs sucessfully on a large
variety of computers under many operation systems, including MacOS,
MS-DOS,
UNIX, and VMS.  Precompiled executables are provided for MacOS and MS-DOS.
For UNIX and VMS system specific files for automated compilation are
provided.

PUZZLE is distributed electronically over the Internet:

- European Bioinformatics Institute
  (Hinxton Hall, Hinxton, Cambridge CB10 1RQ, UK)
  ftp://ftp.ebi.ac.uk/pub/software/mac/puzzle
  ftp://ftp.ebi.ac.uk/pub/software/dos/puzzle
  ftp://ftp.ebi.ac.uk/pub/software/unix/puzzle
  ftp://ftp.ebi.ac.uk/pub/software/vms/puzzle

- FTP server of the work group of the authors
  (Zoological Institute, University of Munich, Munich, FRG)
  ftp://fx.zi.biologie.uni-muenchen.de/pub/puzzle




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