The BioInformer nr. 1, 1997 -- CEPH genotype database 8.1




	A publication of EMBL - Outstation Hinxton, The European Bioinformatics Institute


		Puzzle 3.0 -- maximum likelihood analysis for nucleotide and amino acid alignments PUZZLE is an application 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. Rate heterogenity (invariable sites plus Gamma distributed rates) is incorporated in all models of substitution available (nucleotides: TN, HKY, F84, and submodels; amino acids: Dayhoff, JTT, mtREV24). All model parameters including rate heterogeneity can be estimated from the data by maximum likelihood. PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. In addition, PUZZLE offers a novel method, likelihood mapping, to investigate the support of internal branches without computing an overall tree. PUZZLE is written as an ANSI C program. This means that it will run on most personal computers and workstations if compiled by an appropriate C compiler. Precompiled executables are available for MacOS and MS-DOS. UNIX and VMS makefiles are also provided. New in PUZZLE 3.0 Rate heterogenity included in all models of substitution (Gamma distribution plus invariable sites). Likelihood mapping analysis with Postscript output. Much more sophisticated maximum likelihood parameter estimation for all model parameters including those of rate heterogenity. Codon positions selectable. Update to mtREV24. Less verbose runtime messages. HTML documentation. Better internal error classification. More information in outfile (number of constant positions etc.). Availability PUZZLE is available free of charge for UNIX, VMS, MAcOS and MS-DOS. Announced by: Korbinian Strimmer Resources and further information: PUZZLE Home page http://www.zi.biologie.uni-muenchen.de/~strimmer/puzzle.ht ml PUZZLE software http://www.zi.biologie.uni-muenchen.de/~strimmer/sof tware.html PUZZLE software via FTP (mirror at EBI, UK) UNIX ftp://ftp.ebi.ac.uk/pub/software/unix/puzzle/ MS-DOS ftp://ftp.ebi.ac.uk/pub/software/dos/puzzle/ MacOS ftp://ftp.ebi.ac.uk/pub/software/mac/puzzle/ VMS ftp://ftp.ebi.ac.uk/pub/software/vax/puzzle/ Online manual http://www.zi.biologie.uni-muenchen.de/~strimmer/ma nual.html Contact: Korbinian Strimmer, e-mail: strimmer@zi.biologie.uni-muenchen.de External sites are not endorsed by EMBL-EBI

Direct questions or comments to Bioinformer Editor. This page last modified Friday, 16 July, 1999.
ISSN 1462-1363. More information about the BioInformer.