PUZZLE 2.4 estimates Ts/Tv ratio from data
strimmer at zi.biologie.uni-muenchen.de
Tue Jan 23 05:06:29 EST 1996
PUZZLE VERSION 2.4 NOW AVAILABLE!!
Some *very* useful new features have been added to the PUZZLE program,
partially due to requests of users of earlier versions:
* AUTOMATIC RECOGNITION OF THE DATA TYPE.
Depending on the input file PUZZLE switches automatically to the
nucleotide or amino acid mode.
* AUTOMATIC SELECTION OF THE MODEL OF SEQUENCE EVOLUTION.
If the data set contains amino acids PUZZLE recogizes whether the amino
acids are encoded on mtDNA or on nuclear DNA and selects accordingly one
of the corresponding models of sequence evolution (Dayhoff, JTT, mtREV).
If the data set consists of nucleotides the transition/transversion
parameter is estimated by a maximum likelihood prodedure from the data.
Thus, the Ts/Tv parameter needs not to be specified!
* CHI^2 TEST ON BASE COMPOSITION.
PUZZLE checks with the help of a 5% level chi^2 test whether the base
composition of each taxon is identical with the average that serves as a
basis for the maximum likelihood computation and lists all deviating taxa.
* PLOT OF QUARTET PUZZLING TREE.
PUZZLE plots a picture of the quartet puzzling tree into the "outfile"
and writes a NH tree to the "treefile". External programs ("CONSENSE")
are no more needed.
SOME WORDS ABOUT PUZZLE AND QUARTET PUZZLING:
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 that can be formed from n sequences. The
quartet trees serve as starting points to reconstruct a set of optimal n-taxa
trees. The majority-rule consensus of these trees defines the quartet puzzling
tree and shows groupings that are well supported. More details will be published
elsewhere (K. Strimmer and A. von Haeseler, 1996, Quartet puzzling: A quartet
maximum likelihood method for reconstructing tree topologies, Submitted).
The main advantage of quartet puzzling over almost all other tree reconstruction
methods is that it returns only a completely resolved tree if the phylogenetic
information contained in the data is sufficient. Otherwise a multifurcating
tree is constructed. Another advantage of quartet puzzling is the evaluation of
reliability values for each internal branch. Though quartet puzzling is based
on maximum likelihood it is much faster than any other tree reconstruction method
where maximum likelihood is involved, and it can be applied to data sets with a
large number of taxa.
PUZZLE runs successfully on all popular systems (MacOS, MS-DOS, VMS, UNIX).
Precompiled executables are provided for MacOS and MS-DOS. For UNIX and VMS
system specific files for automated compilation are provided.
* FTP server of the work group of the authors
(Zoological Institute, University of Munich, Munich, FRG)
* European Bioinformatics Institute
(Hinxton Hall, Hinxton, Cambridge CB10 1RQ, UK)
Korbinian Strimmer strimmer at zi.biologie.uni-muenchen.de
Arndt von Haeseler arndt at zi.biologie.uni-muenchen.de
Voice: +49-89-5902-327 Fax: +49-89-5902-474
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