The RAPDistance
Package
Current version 1.04 posted
6th September 1996. The relatedness of DNA samples may be assessed
by comparing RAPD (Randomly Amplified Polymorphic DNA) or RFLP
(Restriction Length Polymorphism) fragments of DNA; these are
obtained from each sample, are separated according to their sizes,
and the presence/absence of shared fragments used to estimate
the relatedness of the DNA samples.
The RAPDistance programs
are designed to help record and analyse the fragment data; the
program prompts are written for RAPD data but the programs can
be used with care for RFLP data. There is a program for encoding
the primary data (presence/absence of bands), and others for editing
the resulting file. Alternatively the data can be recorded using
a spreadsheet program, and transformed into the format used by
these programs, or vice versa.
The primary data may then
be used to calculate pairwise distances between the samples using
one or other of several metrics, and the distances stored in files
with formats for:
- the NJTREE or NTSYS tree-building programs;
- the matrix-comparing program DIPLOMO;
- the statistical analysis program WINAMOVA;
- the phylogenetic analysis programs PAUP and PHYLIP;
- the multivariate analysis programs NTSYS;
The programs are written
in Ansi C. They were developed using Borlands C++ Version 3. The
aim has been to permit the package to operate over the widest
possible range of IBM compatible personal computers. It is not
necessary to have Windows software or the presence of a numerical
co-processor.
The package uses batch files accessed from Main and sub-menus.
There are specific HELP files for each group of programs.
The archive contains 7
files INTRO.DOC, MAC.DOC, README.DOC, RAPD104.ZIP, RAPD104A.ZIP,
RAPD104B.ZIP and RAPD104C.ZIP. The first 3 are ASCII files. The
fourth RAPD103.ZIP is a BINARY file and it is the only one you
need to copy as it contains the following three files. IT MUST
BE TRANSFERRED IN BINARY MODE. The file size is approx 1.156 Mb,
and you may find it is better to retrieve it during the 'quiet'
hours.
The three files RAPD104A/B/C
are an alternative to RAPD104.ZIP. Their lengths are approx 124kb,
592kb and 440kb and can be used if you fail to transfer RAPD104.ZIP
because of its size.
Users of Macintosh computers
are advised to read the file MAC.DOC.
DOWNLOAD
programs here
The authors are:
John Armstrong, John.Armstrong@anu.edu.au
Research School of Biological Sciences, Institute of Advanced
Studies, A.N.U., P.O. Box 475, A.C.T., 2601. ph. 61 (0)6 249 2490;
fax. 61 (0)6 249 4437;
Adrian Gibbs, Adrian.Gibbs@anu.edu.au
Research School of Biological Sciences, Institute of Advanced
Studies, A.N.U., P.O. Box 475, A.C.T., 2601. ph. 61 (0)6 249 4211;
fax. 61 (0)6 249 4437;
Rod Peakall, Rod.Peakall@anu.edu.au
Department of Botany and Zoology, A.N.U., P.O. Box 4, A.C.T.,
0200. ph. 61 (0)6 249 0022; fax. 61 (0)6 249 5573;
Georg Weiller, Georg.Weiller@anu.edu.au
Research School of Biological Sciences, Institute of Advanced
Studies, A.N.U., P.O. Box 475, A.C.T., 2601. ph. 61 (0)6 249 5916;
fax. 61 (0)6 249 4437;
Back to Top
|
