Restriction Data and Phylogenetic Analysis
(c) Copyright 1994 by Tatsuya Ota and the Pennsylvania State University. Permission is granted to copy this document provided that no fee is charged for it and that this copyright notice is not removed. RESTDATA is distributed free of charge by:
|Institute of Molecular Evolutionary Genetics
The Pennsylvania State University
328 Mueller Laboratory
University Park, PA 16802, USA
RESTDATA is designed to compute the following:
For restriction site data:
The numbers of nucleotide substitutions per site for pairs of DNA sequences and their standard errors (Nei and Tajima 1983).
For restriction fragment data:
The numbers of nucleotide substitutions per site for pairs of DNA sequences (Nei and Li 1979). If two or more classes of restriction enzymes are used, the average number of nucleotide substitutions is estimated by the following weighted average of estimates from individual enzymes.
ä mk dk
d = ---------,
where mk and dk is the average number of restriction fragments and the number of nucleotide substitutions estimated for the k-th class of restriction enzymes, respectively.
See Nei (1987, Chapter 5 pp96-110) and the references therein for details of the methods Used in this software.
The software also constructs phylogenetic trees (dendrograms) by using the neighbor-joining (NJ) method (Saitou and Nei 1987) and the unweighted pair group method with arithmetic mean (UPGMA) (Sneath and Sokal 1973) from estimates of the numbers of nucleotide substitutions. Bootstrap tests (Efron 1982, Felsenstein 1985) for these trees can be performed by resampling restriction enzymes. The tests are available only for restriction site data, when data from ten or more restriction enzymes are listed separately in the input file. The test in this program is conducted as described in MEGA (Kumar et al. 1993) rather than in Felsenstein (1985). Please note that the test is not reliable if only a small number of restriction enzymes are used.
This software contains two programs: (1) RESTD.EXE and (2) TREEVIEW.EXE. The first program is written in C language by T.Ota, whereas the second program is written in the modula-2 language by Koichiro Tamura.
First make sure that the diskette you have received contains the following files.
The first two files contain the executable programs. The last two files are data files (examples).
To install RESTDATA on your computer's hard disk drive ("C" drive given here, for example), you should create a directory where the two executable programs will be present. To do this, type the following
C:\MD RESTDATA (Enter)
To copy the RESTDATA programs and files onto your hard disk drive, insert the floppy disk containing the programs into your floppy drive ("A" drive given here, for example). Then, enter the following command
C:\ copy A:*.* C:\RESTDATA (Enter)
If your computer does not have a hard disk, you can use the distribution diskette in your "A" drive.
Efron, B. (1982) The jackknife, the bootstrap, and other resampling plans. CBMS-NSF. Regional conference series in applied mathematics. No 38. Society for industrial and applied mathematics. Philadelphia, PA.
Felsenstein, J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
Kumar, S., K. Tamura, and M. Nei (1993) MEGA: Molecular Evolutionary Genetics Analysis, version 1.01. The Pennsylvania State University, University Park, PA 16802.
Nei, M. (1987) Molecular Evolutionary Genetics. New York: Columbia University.
Nei, M. and W.-H. Li (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 76:5269-5273.
Nei, M. and F. Tajima (1983) Maximum likelihood estimation of the number of nucleotide substitutions for restriction sites data. Genetics 105:207-216.
Saitou, N. and M. Nei (1987) The neighbor-joining method: A new method for reconstructing phylogenetic tree. Mol. Biol. Evol. 4:406-425.
Sneath, P.H.A. and R.R. Sokal (1973) Numerical Taxonomy. Freeman, San Francisco.
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