new PUZZLE release: TREE-PUZZLE 5.0

Heiko Schmidt hschmidt at elgin.inet.dkfz-heidelberg.de
Mon Oct 30 18:59:23 EST 2000


A new version of the PUZZLE software has been released:


TREE-PUZZLE 5.0
---------------

  Heiko A. Schmidt,   Heidelberg, Germany. 
  Korbinian Strimmer, Oxford, UK. 
  Martin Vingron,     Heidelberg, Germany. 
  Arndt von Haeseler, Leipzig, Germany. 

  October 2000

  http://www.tree-puzzle.de



DESCRIPTION
-----------

TREE-PUZZLE is a computer program to reconstruct phylogenetic trees 
from molecular sequence data by maximum likelihood. 
It implements a fast tree search algorithm, quartet puzzling, that allows 
analysis of large data sets and automatically assigns estimations of 
support to each internal branch. TREE-PUZZLE also computes pairwise 
maximum likelihood distances as well as branch lengths for user 
specified trees. Branch lengths can also be calculated under the 
clock-assumption. 
In addition, TREE-PUZZLE offers likelihood mapping, a method 
to investigate the support of a hypothesized internal branch without 
computing an overall tree and to visualize the phylogenetic content 
of a sequence alignment.
TREE-PUZZLE also conducts a number of statistical tests on the data set 
(chi-square test for homogeneity of base composition, likelihood ratio
to test the clock hypothesis, Kishino-Hasegawa test). 
The models of substitution provided by TREE-PUZZLE are TN, HKY, F84, SH for
nucleotides, Dayhoff, JTT, mtREV24, BLOSUM 62, VT, WAG for amino acids, 
and F81 for two-state data. Rate heterogeneity is modelled by a discrete 
Gamma distribution and by allowing invariable sites. The corresponding 
parameters can be inferred from the data set. 


CHANGES
-------

What's new in TREE-PUZZLE 5.0:

 - Puzzle tree reconstruction part is now parallelized using the MPI standard 
   (Message Passing Interface). 

 - Possibility added to specify the names of the input file and the user 
   tree file at the command line. 
   Output files renamed to the form PREFIX.EXTENSION, where PREFIX is the 
   input file name or, if used, the user tree file name. 
   The EXTENSION could be one of the following: puzzle (PUZZLE report), 
   tree (tree file), dist (ML distance file), eps (likelihood mapping output 
   in eps format), qlist (bad quartets), qstep (puzzling step tree IDs as 
   they occur in the analysis), or qtorder (sorted unique list of puzzling 
   step trees). 

 - The tree likelihood value is added to the treefile as a leading comment 
   ("[ lh=x.xxx ]") to the tree string. 

 - VT (variable time) matrix (Mueller and Vingron, 2000) and WAG matrix 
   (Whelan and Goldman, 2000) are added to the AA substitution models. 

 - The Data type and AA-model options in the menu now show the automatically 
   set type/model first. These can now be changed by using the 'd' or 'm' key 
   independently from the type/model selected. This makes it possible to 
   select a desired AA substitution model or data type by piping letters to 
   the standard input without knowing PUZZLE's preselection. 

 - Parameters are written to file when estimated before evaluation of the 
   quartets. 
 
 - The inconsistency with respect to other programs in handling invariable 
   sites has been fixed. 

 - Some minor bug fixes (e.g. the clockbug and another in the optimization 
   routine have been fixed). 

 - Source code organization adopted to the GNU standards
   (configure, make, make install under UNIX)

AVAILABILITY
------------

TREE-PUZZLE is available free of charge from

   http://www.tree-puzzle.de/                      (TREE-PUZZLE home page) 
   http://www.dkfz-heidelberg.de/tbi/tree-puzzle/  (home page mirror at DKFZ) 

or from one of the following places soon

   http://iubio.bio.indiana.edu/soft/molbio/evolve (IUBio archive www, USA) 
   ftp://iubio.bio.indiana.edu/molbio/evolve       (IUBio archive ftp, USA) 
   ftp://ftp.ebi.ac.uk/pub/software                (EBI, UK) 
   ftp://ftp.pasteur.fr/pub/GenSoft                (Institut Pasteur, France) 


TREE-PUZZLE is written in ANSI C. It will run on most personal computers and
workstations if compiled by an appropriate C compiler. Executables are 
available for MacOS and Windows. UNIX and VMS makefiles are also provided.


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Heiko Schmidt             
Deutsches Krebsforschungszentrum    Tel:   + 49 + 6221 / 42-2719
Theoretische Bioinformatik (H0300)  Fax:   + 49 + 6221 / 42-2849
Im Neuenheimer Feld 280             email: ha.schmidt at web.de
D-69120 Heidelberg                  URL:   http://www.DKFZ-Heidelberg.de/tbi
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