This came through an evolutionary biology list. I thought it might be of some interest to loci folks. ---------- Forwarded message ---------- Date: Mon, 10 Apr 00 02:20:04 EDT From: Evoldir <evoldir at evol.biology.McMaster.CA> Reply-To: a.rodrigo at auckland.ac.nz To: stein at fmnh.org Subject: Other: vCEBL 0.3a^V virtual Computational and Evolutionary Biology Laboratory (vCEBL 0.3a) ----------------------------------------------------------------------- We are pleased to announce the release of vCEBL 0.3a. vCEBL builds a graphical user interface around a functional programming language designed specifically for evolutionary analyses. In future releases of vCEBL, users will be able to write single-line scripts that perform complex simulations or analyses using pre-existing primitive or user-supplied functions. In this alpha-release of vCEBL, we provide the basic user-interface, along with four suites of programs (or Packages) installed. Each package contains a different collection of available tools. The four packages are the Analysis, Simulation, Likelihood, and Input/Output packages. The following analyses and tools are available in vCEBL 0.3a: * Construction of serial sample phylogenies using sUPGMA or sWPGMA with sampling times known exactly or ordinally. * Construction of Neighbor-Joining, UPGMA and WPGMA phylogenies. * Estimation of pairwise distance matrices using user-specified rate matrices including general time-reversible models but not including site-to-site heterogeneity in rates. * Estimation of population parameters including substitution/mutation rates using pairwise distances with or without parametric bootstrap confidence intervals. * Maximum-likelihood branch-length optimization of user-specified unconstrained, clock-constrained or serial-sample clock-constrained trees. * ML estimation of divergence between serial samples assuming constant or varying mutation rates. * Simulation of genealogies and sequences under a constant-sized population model with or without serial sampling. Self-installing versions of vCEBL for Macintosh or Windows 95/98 can be obtained from: http://www.cebl.auckland.ac.nz/pages/vcebl.html Users will require JAVA VM 1.1.1 or higher to run vCEBL. The Applet version of vCEBL lacks the Likelihood and Input/output packages. Since vCEBL incorporates sUPGMA, the latter has been removed from our website. Details of the CEBL language can be obtained by contacting one of us through our website (http://www.cebl.auckland.ac.nz). We would greatly appreciate any feedback including bug-reports and wishlists. Allen Rodrigo Alexei Drummond Matthew Goode Computational and Evolutionary Biology Laboratory School of Biological Sciences, University of Auckland Auckland, New Zealand ******************************************************* School of Biological Sciences University of Auckland Private Bag 92019 Auckland, New Zealand Tel: 64-9-3737 599 Ext 7296 Fax: 64-9-3737 414 eFax (US): 1-413-826 5970 Email: a.rodrigo at auckland.ac.nz URL: www.cebl.auckland.ac.nz ******************************************************* ----------------------------------- J. Steinbachs, Ph.D. Computational Biologist Dept of Botany The Field Museum Chicago, IL 60605-2496 office: 312-665-7810 fax: 312-665-7158 http://cb.fmnh.org -----------------------------------