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README.md

NCL - the NEXUS Class Library

Build Status

This is version 2.1.21-dev of NCL by Paul O. Lewis (and others see below)

This git repo was forked from https://github.com/mtholder/ncl so that all of the open tree of life developers would have write permissions. Mark is adding several example programs for dealing with trees from the Open Tree project. They are being added to this repo just because it is easier to distribute NCL-dependent code as a part of the library than it is to document the procedure of installing C++ libraries and linking to them. If we keep using these tools, we can fairly easily pull out these examples as free standing client repo(s).

If we find any changes need to be made to the existing files in the ncl subdir, we should try to remember to pull those back into the mtholder fork of the repo so that other users of NCL can benefit.

Most documentation for this C++ class library is in the form of HTML files in the html directory. Please begin by viewing the html/index.html file in your web browser.

See the INSTALL file for important information about building and installing the NCL and example programs, and incorporating the NCL into your own applications.

As of March 09, 2012, NCL is available under a Simplified BSD license (see BSDLicense.txt) in addition to the GPL license.

ACKNOWLEDGEMENTS

NCL AUTHORS -- the author of the NEXUS Class Library (NCL) version 2.0 is

Paul O. Lewis, Ph.D. Department of Ecology and Evolutionary Biology The University of Connecticut 75 North Eagleville Road, Unit 3043 Storrs, CT 06269-3043 U.S.A.

WWW: http://lewis.eeb.uconn.edu/lewishome Email: paul.lewis@uconn.edu

Versions after 2.0 contain changes primarily made by: Mark T. Holder mholder@users.sourceforge.net

Other contributors to these versions include: Derrick Zwickl Brian O'Meara Brandon Chisham François Michonneau Jeet Sukumaran

Chris Desjardins (https://github.com/cdesjardins) provided the cmake files.

The code in examples/phylobase... was written by Brian O'Meara and Derrick Zwickl for phylobase.

David Suárez Pascal contributed SWIG bindings which heavily influenced those found in branches/v2.2. Thanks to David for blazing the way on the swig binding, Google for funding, and NESCent (in particular Hilmar Lapp) for getting the NESCent GSoC program going.

The 2010 GSoC effort also led to enhancements in terms of annotation storage and xml parsing which are currently on. Michael Elliot contributed some code to the branches/xml branch. Thanks to NESCent and Google for supporting that work.

Many of the files used for testing were provided by Arlin Stoltzfus (see http://www.molevol.org/camel/projects/nexus/ for more information), the Mesquite package, and from TreeBase (thanks, Bill Piel!).

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