Announcement: Tree reconstruction with Puzzle 2.1

Korbinian Strimmer strimmer at
Thu Aug 31 12:12:18 EST 1995

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

    Puzzle version 2.1 is now available on the anonymous ftp site (
    Documentation, ANSI C code with UNIX Makefile, and Mac and
    PowerMac executables are located at /pub/puzzle.


Puzzle is a PHYLIP compatible program that implements the quartet
puzzling method for reconstructing tree topologies from nucleic
and protein sequence 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 will be published elsewhere.


Quartet puzzling was presented at the phylogenetic workshop 1995 in
Bielefeld, Germany, where Puzzle version 1.0 was distributed.
Puzzle version 2.0 was a completely rewritten version of Puzzle 1.0
merging the maximum likelihood program and the quartet puzzling program
into one user friendly program.  Puzzle 2.0 was distributed
Puzzle 2.1 implements a slightly improved quartet puzzling algorithm.
The meaning of the transition/transversion parameter is now to that
in PHYLIP DNAML (was identical to MOLPHY NucML).
Some minor bugs are fixed.


Arndt von Haeseler
Korbinian Strimmer

Zoologisches Institut
Universitaet Muenchen
Luisenstrasse 14
D-80333 Muenchen

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

arndt at
strimmer at

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