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.