[Pipet Devel] virtual computational and evolutionary biology laboratory (vCEBL 0.3a) 0.3a)

Jennifer Steinbachs stein at fmnh.org
Mon Apr 10 08:45:43 EDT 2000

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

* 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:


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

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