Puzzle version 2.2 available

Korbinian Strimmer strimmer at zi.biologie.uni-muenchen.de
Wed Oct 11 07:41:09 EST 1995

                       A N N O U N C E M E N T

    Puzzle version 2.2 is now available on the anonymous ftp site
    fx.zi.biologie.uni-muenchen.de (
    Documentation, ANSI C code with UNIX Makefile, and Mac and
    PowerMac executables are located at /pub/puzzle
    (on the WWW: ftp://fx.zi.biologie.uni-muenchen.de/pub/puzzle
    Puzzle version 2.2 has been tested on Macintosh (68k and PPC)
    personal computers and on Sun, IBM, HP, and Cray workstations.
    As Puzzle is completely written in ANSI C it should run on many
    other platforms.

    Puzzle is PHYLIP compatible, it has the "look and feel" of a
    PHYLIP program and reads PHYLIP sequential formatted data.


Puzzle (NucPuzzle, ProtPuzzle) is an ANSI C 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
reconstruction to all possible quartets and subsequently tries to
combine most of the four-species maximum likelihood trees to construct
an overall tree.  Usually there are several equally good solutions.
A consensus tree generated from the quartet puzzling trees shows which
nodes are well supported.  More details are being published elsewhere
(K. Strimmer and A. von Haeseler.  1995.  Quartet puzzling: A quartet
maximum likelihood method for reconstructing tree topologies).

Puzzle version 2.2 supports the maximum likelihood calculation for
all popular models of nucleotide and protein sequence evolution.


1.0  Quartet puzzling was presented at the phylogenetic workshop 1995
     in Bielefeld, Germany, where Puzzle version 1.0 for doing
     nucleotide and protein sequence analysis was distributed.

2.0  Puzzle version 2.0 was a completely rewritten version of Puzzle
     version 1.0 merging the maximum likelihood program and the
     quartet puzzling program into one user friendly program.
     Puzzle 2.0 was distributed electronically.

2.1  Puzzle 2.1 implemented a slightly changed quartet puzzling
     algorithm. The meaning of the transition/transversion parameter
     was made identical to that in PHYLIP DNAML (was identical to
     MOLPHY NucML).  Some minor bugs were fixed.

2.2  Puzzle version 2.2 has a new optimized internal data structure so
     that Puzzle now needs less RAM resources.  A new quartet puzzling
     algorithm  ("Use selected quartets") has been optionally added.


Arndt von Haeseler
Korbinian Strimmer

Zoologisches Institut
Universitaet Muenchen
Luisenstrasse 14
D-80333 Muenchen

Phone: +49-89-5902327
Fax:   +49-89-5902474

arndt at zi.biologie.uni-muenchen.de
strimmer at zi.biologie.uni-muenchen.de

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