Bug#560347: RFP: ncl -- Nexus Class Library
* Package name : ncl (Nexus Class Library)
Version : 2.1.08 (dated 2009-11-30)
Upstream Author : Paul O. Lewis
* URL or Web page : http://hydrodictyon.eeb.uconn.edu/ncl/
* License : GPL-2
Description : Nexus Class Library
The NEXUS Class Library (NCL) is an integrated collection of C++ classes
designed to allow the user to quickly write a program that reads
NEXUS-formatted data files. It also allows easy extension of the NEXUS format
to include new blocks of your own design.
The NEXUS data file format was specified in the publication cited
below. Please read this paper for further information about the format
specification itself; the documentation for the NCL does not attempt to
explain the structure of a NEXUS data file.
Maddison, D. R., D. L. Swofford, and Wayne P. Maddison. 1997. NEXUS: an
extensible file format for systematic information. Systematic Biology 46(4):
The basic goal of the NCL is to provide a relatively easy way to endow a
C++ program with the ability to read NEXUS data files. The steps necessary
to use the NCL to create a bare-bones program that can read a NEXUS data
file are simple and few, and it is hoped that the availability of this
class library will encourage the use of the NEXUS format. This will in
turn encourage consistency in how programs read NEXUS files and how
programs respond to errors in data files.
There are a large number of special data file formats in use. This places
an extra burden on the end user, who must deal with an increasing number
of file formats all differing in a number of ways. To convert one's data
file to another file format often involves manual manipulation of the
data, an activity that is inherently dangerous and probably has resulted
in the corruption of many data files. At the very least, the large number
of formats in existance has led to a proliferation of data file
variants. With many copies of a given data file on a hard disk, each
formatted differently for various analysis programs, it becomes very easy
to change one (say, correct a datum found to be in error) and then fail to
correct the other versions. The NEXUS file format provides a means for
keeping one master copy of the data and using it with several programs
without modification. The NCL provides a means for encouraging programmers
to use the NEXUS file format in future programs they write.
I could use that for some R packaging (of 'phylobase'), but as I don't use
this directly I don't really want to be / should be the maintainer.
Any biologists in the readership who would like to work on this?
Three out of two people have difficulties with fractions.